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No iron fertilization in the equatorial Pacific Ocean during the last ice age

The equatorial Pacific Ocean is one of the major high-nutrient, low-chlorophyll regions in the global ocean. In such regions, the consumption of the available macro-nutrients such as nitrate and phosphate is thought to be limited in part by the low abundance of the critical micro-nutrient iron1. Greater atmospheric dust deposition2 could have fertilized the equatorial Pacific with iron during the last ice age—the Last Glacial Period (LGP) but the effect of increased ice-age dust fluxes on primary productivity in the equatorial Pacific remains uncertain. Here we present meridional transects of dust (derived from the 232Th proxy), phytoplankton productivity (using opal, 231Pa/230Th and excess Ba), and the degree of nitrate consumption (using foraminifera-bound δ15N) from six cores in the central equatorial Pacific for the Holocene (0–10,000 years ago) and the LGP (17,000–27,000 years ago). We find that, although dust deposition in the central equatorial Pacific was two to three times greater in the LGP than in the Holocene, productivity was the same or lower, and the degree of nitrate consumption was the same. These biogeochemical findings suggest that the relatively greater ice-age dust fluxes were not large enough to provide substantial iron fertilization to the central equatorial Pacific. This may have been because the absolute rate of dust deposition in the LGP (although greater than the Holocene rate) was very low. The lower productivity coupled with unchanged nitrate consumption suggests that the subsurface major nutrient concentrations were lower in the central equatorial Pacific during the LGP. As these nutrients are today dominantly sourced from the Subantarctic Zone of the Southern Ocean, we propose that the central equatorial Pacific data are consistent with more nutrient consumption in the Subantarctic Zone, possibly owing to iron fertilization as a result of higher absolute dust fluxes in this region7,8. Thus, ice-age iron fertilization in the Subantarctic Zone would have ultimately worked to lower, not raise, equatorial Pacific productivity.

Publication type: 
Author: 
Kassandra Maria Costa
Jerry F. McManus
Robert F. Anderson
H. Ren
D. M. Sigman
Gisela Winckler
Martin Q. Fleisher
F. Marcantonio
A. Christina Ravelo
Subjects: 
Biogeochemistry
Paleoceanography
Glacial epoch
Iron
Title string: 
No iron fertilization in the equatorial Pacific Ocean during the last ice age
GUID update: 
https://academiccommons.columbia.edu/catalog/ac:mw6m905qj3

Beyond syndromic management: Opportunities for diagnosis-based treatment of sexually transmitted infections in low- and middle-income countries

Introduction
In light of the limited impact the syndromic management approach has had on the global sexually transmitted infection (STI) epidemic, we assessed a care model comprising point-of-care (POC) STI testing, immediate treatment, and expedited partner therapy (EPT) among a cohort of young women at high HIV risk in South Africa.

Methods and findings
HIV negative women presenting for STI care underwent POC testing for Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Trichomonas vaginalis (TV), and swabs were sent for NG culture and susceptibility testing. Results were available within 2 hours and women with STIs were immediately treated and offered EPT packs, including medication, condoms, and information for sexual partners. An EPT questionnaire was administered after one week, and women retested for STIs after 6 and 12 weeks. 267 women, median age 23 (IQR 21–26), were recruited and 88.4% (236/267) reported genital symptoms. STI prevalence was CT 18.4% (95%CI 13.7–23.0), NG 5.2% (95%CI 2.6–7.9) and TV 3.0% (95%CI 1.0–5.0). After 12 weeks, all but one NG and two CT infections were cleared. No cephalosporin-resistant NG was detected. Of 63/267 women (23.6%) diagnosed with STIs, 98.4% (62/63) were offered and 87.1% (54/62) accepted EPT. At one week 88.9% (48/54) stated that their partner had taken the medication. No allergic reactions or social harms were reported. Of 51 women completing 6-week follow up, detection rates were lower amongst women receiving EPT (2.2%, 1/46) compared to those who did not (40.0%, 2/5), p = 0.023. During focus group discussions women supported the care model, because they received a rapid, specific diagnosis, and could facilitate their partners’ treatment.

Conclusions
POC STI testing and EPT were acceptable to young South African women and their partners, and could play an important role in reducing STI reinfection rates and HIV risk. Larger studies should evaluate the feasibility and cost-effectiveness of implementing this strategy at population level.

Topic: 
Publication type: 
Author: 
Nigel J. Garrett
Farzana Osman
Bhavna Maharaj
Nivashnee Naicker
Andrew Gibbs
Emily Norman
Natasha Samsunder
Hope Ngobese
Nireshni Mitchev
Ravesh Singh
Abdool Salim Karim
Ayesha B. M. Kharsany
Koleka P. Mlisana
Anne Rompalo
Adrian Mindel
Subjects: 
Sexual health
Sexually transmitted diseases--Treatment
Epidemiology
HIV infections—Prevention
Title string: 
Beyond syndromic management: Opportunities for diagnosis-based treatment of sexually transmitted infections in low- and middle-income countries
GUID update: 
https://academiccommons.columbia.edu/catalog/ac:95x69p8d16

Readmission prediction via deep contextual embedding of clinical concepts

Objective
Hospital readmission costs a lot of money every year. Many hospital readmissions are avoidable, and excessive hospital readmissions could also be harmful to the patients. Accurate prediction of hospital readmission can effectively help reduce the readmission risk. However, the complex relationship between readmission and potential risk factors makes readmission prediction a difficult task. The main goal of this paper is to explore deep learning models to distill such complex relationships and make accurate predictions.

Materials and methods
We propose CONTENT, a deep model that predicts hospital readmissions via learning interpretable patient representations by capturing both local and global contexts from patient Electronic Health Records (EHR) through a hybrid Topic Recurrent Neural Network (TopicRNN) model. The experiment was conducted using the EHR of a real world Congestive Heart Failure (CHF) cohort of 5,393 patients.

Results
The proposed model outperforms state-of-the-art methods in readmission prediction (e.g. 0.6103 ± 0.0130 vs. second best 0.5998 ± 0.0124 in terms of ROC-AUC). The derived patient representations were further utilized for patient phenotyping. The learned phenotypes provide more precise understanding of readmission risks.

Discussion
Embedding both local and global context in patient representation not only improves prediction performance, but also brings interpretable insights of understanding readmission risks for heterogeneous chronic clinical conditions.

Conclusion
This is the first of its kind model that integrates the power of both conventional deep neural network and the probabilistic generative models for highly interpretable deep patient representation learning. Experimental results and case studies demonstrate the improved performance and interpretability of the model.

Topic: 
Publication type: 
Author: 
Cao Xiao
Tengfei Ma
Adji Bousso Dieng
David Meir Blei
Fei Wang
Subjects: 
Computer science
Hospital utilization--Forecasting
Hospital records
Neural networks (Computer science)
Title string: 
Readmission prediction via deep contextual embedding of clinical concepts
GUID update: 
https://academiccommons.columbia.edu/catalog/ac:6m905qftvz

Blue intensity from a tropical conifer’s annual rings for climate reconstruction: An ecophysiological perspective

We developed Blue Intensity (BI) measurements from the crossdated ring sequences of Fokienia hodginsii (of the family Cupressaceae) from central Vietnam. BI has been utilized primarily as an indirect proxy measurement of latewood (LW) density of conifers (i.e., LWBI) from high latitude, temperature-limited boreal forests. As such, BI closely approximates maximum latewood density (MXD) measurements made from soft x-ray. The less commonly used earlywood (EW) BI (EWBI) represents the minimum density of EW and is influenced by the lighter pixels from the vacuoles or lumens of cells. The correlation of our BI measurements with climate, strongest for EWBI, rivals that for total ring width (RW), and we demonstrate that it can be successfully employed as an independent predictor for reconstruction models. EWBI exhibits robust spatial correlations with winter and spring land temperature, sea surface temperature (SST) over the regional domain of ENSO, and the Standardized Precipitation Evapotranspiration Index (SPEI) over Indochina. However, in order to mitigate the effects of color changes at the heartwood – sapwood boundary we calculated ΔBI (EWBI-LWBI), and it too exhibits a significant (p < 0.05), temporally stable response to prior autumn (Oct-Nov) rainfall and winter (December to April) dry season temperature. We interpret this response as reflecting a potential cavitation defense by reducing lumen diameter as a means to safeguard hydraulic conductivity in the stem, and to prevent the xylem from imploding due to negative pressure. This study has wide implications for the further use of BI from the global tropics, though it is unclear how many tropical tree species will be appropriate for use. It seems very likely that other wood anatomical measurements can be combined with BI and RW for climate reconstruction.

Publication type: 
Author: 
Brendan M. Buckley
Kyle Hansen
Kevin L. Griffin
Stephanie Christine Schmiege
Rose C. Oelkers
D’Rosanne Dorothy Arrigo
Daniel K. Stahle
Nicole K. Davi
Tran Quoc Trung Nguyen
Canh Nam Le
Robert J. Wilson
Subjects: 
Dendrochronology
Monsoons
Cupressaceae
Ecology
Environmental sciences
Title string: 
Blue intensity from a tropical conifer’s annual rings for climate reconstruction: An ecophysiological perspective
GUID update: 
https://academiccommons.columbia.edu/catalog/ac:prr4xgxd4b

A Variant PfCRT Isoform Can Contribute to Plasmodium falciparum Resistance to the First-Line Partner Drug Piperaquine

Current efforts to reduce the global burden of malaria are threatened by the rapid spread throughout Asia of Plasmodium falciparum resistance to artemisinin-based combination therapies, which includes increasing rates of clinical failure with dihydroartemisinin plus piperaquine (PPQ) in Cambodia. Using zinc finger nuclease-based gene editing, we report that addition of the C101F mutation to the chloroquine (CQ) resistance-conferring PfCRT Dd2 isoform common to Asia can confer PPQ resistance to cultured parasites. Resistance was demonstrated as significantly higher PPQ concentrations causing 90% inhibition of parasite growth (IC90) or 50% parasite killing (50% lethal dose [LD50]). This mutation also reversed Dd2-mediated CQ resistance, sensitized parasites to amodiaquine, quinine, and artemisinin, and conferred amantadine and blasticidin resistance. Using heme fractionation assays, we demonstrate that PPQ causes a buildup of reactive free heme and inhibits the formation of chemically inert hemozoin crystals. Our data evoke inhibition of heme detoxification in the parasite’s acidic digestive vacuole as the primary mode of both the bis-aminoquinoline PPQ and the related 4-aminoquinoline CQ. Both drugs also inhibit hemoglobin proteolysis at elevated concentrations, suggesting an additional mode of action. Isogenic lines differing in their pfmdr1 copy number showed equivalent PPQ susceptibilities. We propose that mutations in PfCRT could contribute to a multifactorial basis of PPQ resistance in field isolates.

Publication type: 
Author: 
Satish Kumar Dhingra
Devasha Redhi
Jill M. Combrinck
Tomas Yeo
John Okombo
Philipp P. Henrich
Annie N. Cowell
Purva Gupta
Matthew L. Stegman
Jonathan M. Hoke
Roland A. Cooper
Elizabeth Winzeler
Sachel Shu Li Mok
Timothy J. Egan
David Armand Fidock
Subjects: 
Plasmodium falciparum
Microbiology
Antimalarials
Biology
Title string: 
A Variant PfCRT Isoform Can Contribute to Plasmodium falciparum Resistance to the First-Line Partner Drug Piperaquine
GUID update: 
https://academiccommons.columbia.edu/catalog/ac:cnp5hqbznd

Evolutionary Dynamics of Pandemic Methicillin-Sensitive Staphylococcus aureus ST398 and Its International Spread via Routes of Human Migration

Methicillin-susceptible Staphylococcus aureus (MSSA) accounts for the majority of S. aureus infections globally, and yet surprisingly little is known about its clonal evolution. We applied comparative whole-genome sequencing (WGS) analyses to epidemiologically and geographically diverse ST398-MSSA, a pandemic lineage affecting both humans and livestock. Bayesian phylogenetic analysis predicted divergence of human-associated ST398-MSSA ~40 years ago. Isolates from Midwestern pigs and veterinarians differed substantially from those in New York City (NYC). Pig ST398 strains contained a large region of recombination representing imports from multiple sequence types (STs). Phylogeographic analyses supported the spread of ST398-MSSA along local cultural and migratory links between parts of the Caribbean, North America, and France, respectively. Applying pairwise single-nucleotide polymorphism (SNP) distances as a measure of genetic relatedness between isolates, we observed that ST398 not only clustered in households but also frequently extended across local social networks. Isolates collected from environmental surfaces reflected the full diversity of colonizing individuals, highlighting their potentially critical role as reservoirs for transmission and diversification. Strikingly, we observed high within-host SNP variability compared to our previous studies on the dominant methicillin-resistant Staphylococcus aureus (MRSA) clone USA300. Our data indicate that the dynamics of colonization, persistence, and transmission differ substantially between USA300-MRSA and ST398-MSSA. Taken together, our study reveals local and international routes of transmission for a major MSSA clone, indicating key impacts of recombination and mutation on genetic diversification and highlighting important ecological differences from epidemic USA300. Our study demonstrates extensive local and international routes of transmission for a major MSSA clone despite the lack of substantial antibiotic resistance.

Publication type: 
Author: 
Anne Uhlemann-Catrin
Paul R. McAdam
Sean B. Sullivan
Justin R. Knox
Hossein Khiabanian
Raul Rabadan
Peter R. Davies
J. Ross Fitzgerald
Franklin D. Lowy
Subjects: 
Staphylococcus aureus
Genomes--Data processing
Human beings--Migrations
Systems biology
Title string: 
Evolutionary Dynamics of Pandemic Methicillin-Sensitive Staphylococcus aureus ST398 and Its International Spread via Routes of Human Migration
GUID update: 
https://academiccommons.columbia.edu/catalog/ac:8931zcrjg6

Viral Diversity of House Mice in New York City

The microbiome of wild Mus musculus (house mouse), a globally distributed invasive pest that resides in close contact with humans in urban centers, is largely unexplored. Here, we report analysis of the fecal virome of house mice in residential buildings in New York City, NY. Mice were collected at seven sites in Manhattan, Queens, Brooklyn, and the Bronx over a period of 1 year. Unbiased high-throughput sequencing of feces revealed 36 viruses from 18 families and 21 genera, including at least 6 novel viruses and 3 novel genera. A representative screen of 15 viruses by PCR confirmed the presence of 13 of these viruses in liver. We identified an uneven distribution of diversity, with several viruses being associated with specific locations. Higher mouse weight was associated with an increase in the number of viruses detected per mouse, after adjusting for site, sex, and length. We found neither genetic footprints to known human viral pathogens nor antibodies to lymphocytic choriomeningitis virus.

UNI: 
Publication type: 
Author: 
Simon Hedley Williams
Xiaoyu Che
Joel A. Garcia
John D. Klena
Bohyun Lee
Dorothy R. Muller
Werner Ulrich
Robert M. Corrigan
Stuart T. Nichol
Komal Jain
W. Ian Lipkin
Subjects: 
Microbiology
Microbial ecology
Mice
Viruses
Title string: 
Viral Diversity of House Mice in New York City
GUID update: 
https://academiccommons.columbia.edu/catalog/ac:pc866t1g3z

Dr. Strange Geo-Blocking Love Or: How The E.U. Learned To Stop Worrying About Cultural Integration And Love The TV Trade Barrier

The E.U. Antitrust Case that opened on July 23, 2015 against Sky U.K. and six American studios—Disney, Fox, NBCUniversal, Paramount Pictures, Sony and Warner Brothers—has its structural roots in the Television Without Frontiers Directive, which was vigorously debated as a last-minute standoff that threatened to derail the conclusion of the GATT Uruguay Round of trade negotiations and is still considered to be the cornerstone of the European Union’s audiovisual policy. This Article examines the unique history of a Cultural Exception with respect to audiovisual works as applied in trade negotiations to Hollywood film and television productions, and argues that, rather than violating E.U. regulations, the decades-old practice of regional contractual restrictions and geo-blocking is both consistent with and a direct result of the E.U.’s protectionist and paternalistic efforts to shield its individual member states’ local production entities from competition and its populations from a perceived and decidedly unwelcomed Svengali-like juggernaut of American cultural influence. The E.U. antitrust action is therefore in direct contravention to the spirit of the trade laws over which Hollywood studios were so stridently subjected to debating and is inconsistent with stated E.U. audiovisual norms. Abolishing regional access limitations will put the future of the E.U.’s various local distributors at risk, for the existing patchwork of distribution related rules impacting foreign property directly impacts American producers’ decisions regarding whether and how to continue to do business in the region. Thus, any attempt to implement the E.C.’s aspirational Digital Single Market 2020 target terms must be reconciled in light of the current political climate in Europe and global technological capabilities if the E.U. is to remain a relevant market at the forefront of the modern entertainment industry and continue to benefit from the uniquely privileged relationship it has enjoyed for nearly a century with its many Hollywood studio production partners.

Topic: 
Publication type: 
Author: 
Batia M. Zareh
Subjects: 
Law and art
Television--Law and legislation
Antitrust law
Motion pictures--Law and legislation
Title string: 
Dr. Strange Geo-Blocking Love Or: How The E.U. Learned To Stop Worrying About Cultural Integration And Love The TV Trade Barrier
GUID update: 
https://academiccommons.columbia.edu/catalog/ac:vmcvdncjwv

Suicidal Plans and Attempts Among Adolescents in Mongolia: Urban Versus Rural Differences

Background: Although 75% of suicides occur in low- and middle-income countries, few studies have examined suicidal behaviors among young people in these countries. Aims: This study aimed to examine what individual characteristics were associated with suicidal plans and attempts among Mongolian youth and whether suicidal risks and behaviors varied by urban and rural locations. Method: Logistic regression analyses were utilized to investigate suicidal plans and attempts among 5,393 adolescents using the Global Student Health Survey – 2013. Results: Adolescents who lived in urban areas were at higher risk for suicidal plans and behaviors than those who lived in rural areas; however, the patterns of suicidal risks were similar. Specifically, individual characteristics, such as being female, feeling lonely and worried, smoking cigarettes, drinking alcohol, and having fights at school, were associated with suicidal plans and behaviors regardless of the residential places. Limitations: A number of important variables have not been included in the questionnaire such as depression, family and parental support, household income, family constructs etc. Conclusion: Given the comparable patterns of risk between urban and rural adolescents and the relatively high rates of suicidal plans and attempts, similar mental health services and interventions are necessitated for both urban and rural areas.

Topic: 
UNI: 
Publication type: 
Author: 
Sarantsetseg Davaasambuu
Suvd Batbaatar
Susan S. Witte
Phillip Hamid
Maria A. Oquendo
Marjorie Kleinman
Michael Olivares
Madelyn S. Gould
Subjects: 
Teenagers--Mental health
Teenagers--Suicidal behavior
Psychiatry
Epidemiology
Title string: 
Suicidal Plans and Attempts Among Adolescents in Mongolia: Urban Versus Rural Differences
GUID update: 
https://academiccommons.columbia.edu/catalog/ac:gb5mkkwh95

Piloting a Savings-Led Microfinance Intervention with Women Engaging in Sex Work in Mongolia: Further Innovation for HIV Risk Reduction

This paper describes a pilot study testing the feasibility of an innovative savings-led microfinance intervention in increasing the economic empowerment and reducing the sexual risk behavior of women engaging in sex work in Mongolia. Women’s economic vulnerability may increase their risk for HIV by compromising their ability to negotiate safer sex with partners and heightening the likelihood they will exchange sex for survival. Microfinance has been considered a potentially powerful structural HIV prevention strategy with women conducting sex work, as diversification of income sources may increase women’s capacity to negotiate safer transactional sex. With 50% of all reported female HIV cases in Mongolia detected among women engaging in sex work, direct prevention intervention with women conducting sex work represents an opportunity to prevent a potentially rapid increase in HIV infection in urban Mongolia. The piloted intervention consisted of a matched savings program in which matched savings could be used for business development or vocational education, combined with financial literacy and business development training for women engaging in sex work. Results of the pilot demonstrate participants’ increased confidence in their ability to manage finances, greater hope for pursuing vocational goals, moderate knowledge gains regarding financial literacy, and an initial transition from sex work to alternative income generation for five out of nine participants. The pilot findings highlight the potential for such an intervention and the need for a clinical trial testing the efficacy of savings-led microfinance programs in reducing HIV risk for women engaging in sex work in Mongolia.

Publication type: 
Author: 
Laura Cordisco Tsai
Susan S. Witte
Toivgoo Aira
Batsukh Altantsetseg
Marion Riedel
Subjects: 
Microfinance
HIV infections—Prevention
Public health
Women in economic development
Prostitutes
Title string: 
Piloting a Savings-Led Microfinance Intervention with Women Engaging in Sex Work in Mongolia: Further Innovation for HIV Risk Reduction
GUID update: 
https://academiccommons.columbia.edu/catalog/ac:3bk3j9kd69

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