bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prolonged empirical antibiotic therapy is correlated with bloodstream infections and increased mortality in a tertiary care hospital in Ethiopia: bacteriology testing matters
Authors: Semret Makeda , Abebe Workeabeba , Kong Ling Yuan , Alemayehu Tinsae , Beyene Temesgen , Libman Michael D , Amogne Wondwossen , Johannsen Øystein Haarklau , Gebretekle Gebremedhin B , Seifu Daniel , Yansouni Cedric P 
Published: May 2020

Abstract

Background
Hospital-associated infection (HAI) and antimicrobial resistance (AMR) are major health threats in low- and middle-income countries (LMICs). Because diagnostic capacity is lacking throughout most of Africa, patients are commonly managed with prolonged empirical antibiotic therapy. Our goal was to assess mortality in relation to HAI and empirical therapy in Ethiopia’s largest referral hospital.

Methods
Cohort study of patients with suspected HAI at Tikur Anbessa Specialized Hospital from October 2016 to October 2018. Blood culture testing was performed on an automated platform. Primary outcomes were proportion of patients with bloodstream infection (BSI), antibiotic resistance patterns and 14 day mortality. We also assessed days of therapy (DOT) pre- and post-blood culture testing.

Results
Of 978 enrolled patients, 777 had blood culture testing; 237 (30%) had a BSI. Enterobacteriaceae were isolated in 49%; 81% of these were cephalosporin resistant and 23% were also carbapenem resistant. Mortality at 14 days was 31% and 21% in those with and without BSI, respectively. Ceftriaxone resistance was strongly correlated with mortality. Patients with BSI had longer DOT pre-blood culture testing compared with those without BSI (median DOT 12 versus 3 days, respectively, P &lt; 0.0001). After testing, DOT were comparable between the two groups (20 versus 18 days, respectively).

Conclusions
BSI are frequent and fatal among patients with suspected HAI in Ethiopia. Highly resistant blood isolates are alarmingly common. This study provides evidence that investing in systematic blood culture testing in LMICs identifies patients at highest risk of death and that empirical management is frequently inappropriate. Major investments in laboratory development are critical to achieve better outcomes.
C-terminal aromatic residue of Plasmodium ferredoxin important for the interaction with ferredoxin: NADP(H) oxidoreductase: possible involvement for artemisinin resistance of human malaria parasites
Authors: Kimata-Ariga Yoko , Sakamoto Asako , Kamatani Miho , Saitoh Takashi , Hase Toshiharu 
Published: May 2020

Abstract
The malaria parasite (Plasmodium sp.) contains a plastid-derived organelle called the apicoplast, which is essential for the growth of the parasite. In this organelle, a redox system comprising plant-type ferredoxin (Fd) and Fd: NADP(H) oxidoreductase (FNR) supplies reducing power for the crucial metabolic pathways. Electron transfer between Plasmodium falciparum Fd (PfFd) and FNR (PfFNR) is performed with higher affinity and specificity than those of plant Fd and FNR. We investigated the structural basis for such superior protein–protein interaction by focussing on the Plasumodium-specific regions of PfFd. Significant contribution of the C-terminal region of PfFd for the electron transfer with PfFNR was revealed by exchanging the C-terminal three residues between plant Fd and PfFd. Further site-directed mutagenesis of the PfFd C-terminal residues indicated that the presence of aromatic residue at Positions 96 and 97 contributes to the lower Km for PfFNR. Physical binding analyses using fluorescence and calorimetric measurements supported the results. A mutation from Asp to Tyr at position 97 of PfFd was recently reported to be strongly associated with P. falciparum resistance to artemisinin, the front line anti-malarial drug. Thus, the enhanced interaction of PfFd D97Y protein with PfFNR could be involved in artemisinin resistance of human malaria parasites.
Health Information, Treatment, and Worker Productivity
Authors: Dillon Andrew , Friedman Jed , Serneels Pieter 
Published: May 2020

Abstract
Agricultural and other physically demanding sectors are important sources of growth in developing countries, but prevalent diseases such as malaria can adversely impact the productivity and labor supply of workers. We estimate the impact of malaria infection on worker earnings, labor supply, daily productivity, and task selection by using a phased-in design where we randomize the study week in which piece-rate workers at a large sugarcane plantation in Nigeria are offered malaria testing and treatment. Two estimation strategies indicate a significant and substantial intent to treat effect of the intervention. The program increases worker weekly earnings by 11%–13% over the weeks following the offer, depending on the reference period, estimated using a between-worker estimator that exploits the experimental design. A within-worker estimate provides similar but smaller estimates of 8%–10%. We identify different pathways through which this effect occurs. For workers who test positive for malaria, the treatment of illness principally increases labor supply, leading to higher earnings. For workers who test negative, the health information leads to increased earnings via augmented daily productivity. This productivity response arises, in part, from selection into higher return tasks within their job at the plantation. The results underline the importance of medical treatment but also of improved access to information about one's health status, as the absence of either leads workers to work less or choose lower return tasks when working.
A Sustainable Psychosocial Model to Support the National Investigation and Prosecution of Conflict-related Sexual Violence Crimes
Authors: Bianchini Barbara , Rubert Sara 
Published: May 2020

Abstract
This article presents a psychosocial model that can be used by national jurisdictions to cope with the multiple challenges in prosecuting conflict-related sexual violence crimes. Best practices developed over years of professional experience with victims of crime and trauma survivors guided the authors in developing a trauma-centred approach. In the proposed model, the judiciary plays a central role in empowering survivors of heinous crimes to become active agents of their lives by positively contributing to the quest for justice. The authors aim at offering specific and practical recommendations to investigative and judicial staff dealing with the multifaceted issues arising out of conflict-related sexual violence prosecutions. The hope is to offer a flexible model that can be adapted to different national jurisdictions’ needs, can produce sustainable long-term interventions for survivors’ well-being, and improve the quality of the evidence collected.
Examining Gender Inequality and Armed Conflict at the Subnational Level
Authors: Forsberg Erika , Olsson Louise 
Published: May 2020

AbstractA growing body of quantitative research points to a robust relationship between gender inequality and armed conflict. In order to progress our understanding of this relationship, we make two contributions. First, we identify three potential explanations as to why gender inequality can be associated with conflict—gender inequality norms, societal capacity, and gendered socioeconomic development—and suggest an empirical strategy to gauge the explanatory leverage of each explanation. Second, we offer a more nuanced treatment of the dependent variable at the subnational level, moving beyond a dichotomized view of armed conflict to accounting for both its level and type. We test our hypotheses using district-level data on gender inequality and conflicts in India, covering the 1989–2014 period. Our findings show that the three explanations do not produce the same outcomes in the data. We argue that this speaks to the need to adjudicate between different forms of mechanisms that can connect gender inequality to conflict. Our results show support for women's status being important for understanding a society's capacity to handle conflict nonviolently. On the negative side, gendered socioeconomic developments resulting in a male surplus create conditions conducive for armed conflict, particularly in urban areas. A more surprising finding is that the gender inequality norm, in and of itself, does not appear to have a strong effect on the risk of armed conflict. This does not mean that we can disregard the explanation, but it underlines that there can be inherent problems with this commonly used argument.
RING finger ubiquitin E3 ligase gene TaSDIR1-4A contributes to determination of grain size in common wheat
Authors: Wang Jingyi , Wang Ruitong , Mao Xinguo , Zhang Jialing , Liu Yanna , Xie Qi , Yang Xiaoyuan , Chang Xiaoping , Li Chaonan , Zhang Xueyong , Jing Ruilian 
Published: May 2020

Abstract
Salt and drought-induced RING finger1 (SDIR1) is a RING-type E3 ubiquitin ligase that plays a key role in ABA-mediated responses to salinity and drought stress via the ubiquitination pathway in some plant species. However, its function in wheat (Triticum aestivum) is unknown. Here, we isolated a SDIR1 member in wheat, TaSDIR1-4A, and characterized its E3 ubiquitin ligase activity. DNA polymorphism assays showed the presence of two nucleotide variation sites in the promoter region of TaSDIR1-4A, leading to the detection of the haplotypes Hap-4A-1 and Hap-4A-2 in wheat populations. Association analysis showed that TaSDIR1-4A haplotypes were associated with 1000-grain weight (TGW) across a variety of different environments, including well-watered and heat-stress conditions. Genotypes with Hap-4A-2 had higher TGW than those with Hap-4A-1. Phenotypes in both gene-silenced wheat and transgenic Arabidopsis showed that TaSDIR1-4A was a negative regulator of grain size. Gene expression assays indicated that TaSDIR1-4A was most highly expressed in flag leaves, and expression was higher in Hap-4A-1 accessions than in Hap-4A-2 accessions. The difference might be attributable to the fact that TaERF3 (ethylene response factor) can act as a transcriptional repressor of TaSDIR1-4A in Hap-4A-2 but not in Hap-4A-1. Examination of modern wheat varieties shows that the favorable haplotype has been positively selected in breeding programs in China. The functional marker for TaSDIR1-4A developed in this study should be helpful for future wheat breeding.
Public perception of COVID-19’s global health crisis on Twitter until 14 weeks after the outbreak
Authors: Abdo Muhammad S , Alghonaim Ali S , Essam Bacem A 
Published: May 2020

Abstract
Because language represents advanced aspects of human cognition, studying linguistic styles and figurative meaning have proven effective in measuring embodied cognition about the external world. This article defines the most worrisome topics people discussed from Weeks 1 to 14 after the outbreak and compares the message delivered by the literal use of words to the figurative use of metaphoric expressions. We bootstrapped representative data from Twitter over 14 weeks since the inception of the outbreak to be analyzed thematically using the Linguistic Inquiry and Word Count (LIWC) 2015 software as well as corpus tools. The MetaNet database, corpus tools, and manual annotation were used to detect expressions that can be linguistically mapped to the formalized list of conceptual metaphors. The most frequently tagged themes included ‘the outbreak of the pandemic, its epidemiology, its prophylaxis measures, national and world economies, media’, as well as the ‘signs and symptoms of COVID-19’. Although LIWC-based analysis showed English-speaking tweeters maintained high levels of analytical thinking, elevated levels of anger, anxiety, and doubtfulness, there were discrepancies and improper conceptualization of the clinical picture of the pandemic.
5′ modifications to CRISPR–Cas9 gRNA can change the dynamics and size of R-loops and inhibit DNA cleavage
Authors: Mullally Grace , van Aelst Kara , Naqvi Mohsin M , Diffin Fiona M , Karvelis Tautvydas , Gasiunas Giedrius , Siksnys Virginijus , Szczelkun Mark D 
Published: May 2020

AbstractA key aim in exploiting CRISPR–Cas is gRNA engineering to introduce additional functionalities, ranging from individual nucleotide changes that increase efficiency of on-target binding to the inclusion of larger functional RNA aptamers or ribonucleoproteins (RNPs). Cas9–gRNA interactions are crucial for complex assembly, but several distinct regions of the gRNA are amenable to modification. We used in vitro ensemble and single-molecule assays to assess the impact of gRNA structural alterations on RNP complex formation, R-loop dynamics, and endonuclease activity. Our results indicate that RNP formation was unaffected by any of our modifications. R-loop formation and DNA cleavage activity were also essentially unaffected by modification of the Upper Stem, first Hairpin and 3′ end. In contrast, we found that 5′ additions of only two or three nucleotides could reduce R-loop formation and cleavage activity of the RuvC domain relative to a single nucleotide addition. Such modifications are a common by-product of in vitro transcribed gRNA. We also observed that addition of a 20 nt RNA hairpin to the 5′ end of a gRNA still supported RNP formation but produced a stable ∼9 bp R-loop that could not activate DNA cleavage. Consideration of these observations will assist in successful gRNA design.
InMeRF: prediction of pathogenicity of missense variants by individual modeling for each amino acid substitution
Authors: Takeda Jun-ichi , Nanatsue Kentaro , Yamagishi Ryosuke , Ito Mikako , Haga Nobuhiko , Hirata Hiromi , Ogi Tomoo , Ohno Kinji 
Published: May 2020

Abstract
In predicting the pathogenicity of a nonsynonymous single-nucleotide variant (nsSNV), a radical change in amino acid properties is prone to be classified as being pathogenic. However, not all such nsSNVs are associated with human diseases. We generated random forest (RF) models individually for each amino acid substitution to differentiate pathogenic nsSNVs in the Human Gene Mutation Database and common nsSNVs in dbSNP. We named a set of our models ‘Individual Meta RF’ (InMeRF). Ten-fold cross-validation of InMeRF showed that the areas under the curves (AUCs) of receiver operating characteristic (ROC) and precision–recall curves were on average 0.941 and 0.957, respectively. To compare InMeRF with seven other tools, the eight tools were generated using the same training dataset, and were compared using the same three testing datasets. ROC-AUCs of InMeRF were ranked first in the eight tools. We applied InMeRF to 155 pathogenic and 125 common nsSNVs in seven major genes causing congenital myasthenic syndromes, as well as in VANGL1 causing spina bifida, and found that the sensitivity and specificity of InMeRF were 0.942 and 0.848, respectively. We made the InMeRF web service, and also made genome-wide InMeRF scores available online (https://www.med.nagoya-u.ac.jp/neurogenetics/InMeRF/).
Hierarchically porous monoliths based on low-valence transition metal (Cu, Co, Mn) oxides: gelation and phase separation
Authors: Lu Xuanming , Kanamori Kazuyoshi , Nakanishi Kazuki 
Published: May 2020

Abstract
Hierarchically porous monoliths based on copper (Cu), cobalt (Co) and manganese (Mn) oxides with three-dimensionally (3D) interconnected macropores and open nanopores were prepared using metal bromides as precursors via a sol–gel process accompanied by phase separation. The difficulty of gelation for low-valence metal cation was overcome by introducing a highly electronegative Br atom near to the metal atom to control the rates of hydrolysis and polycondensation. The 3D interconnected macropores were obtained using appropriate polymers to induce phase separation. The domain sizes of macropores and skeletons can be controlled by reaction parameters such as concentration and/or average molecular weight of polymers, and the amount of hydrochloric acid. The crystalline metal oxide monoliths with their 3D interconnected macroporous structure preserved were obtained after heat treatment in air.
Quantum simulation of particle pair creation near the event horizon
Authors: Wang Yao , Sheng Chong , Lu Yong-Heng , Gao Jun , Chang Yi-Jun , Pang Xiao-Ling , Yang Tian-Huai , Zhu Shi-Ning , Liu Hui , Jin Xian-Min 
Published: May 2020

Abstract
Though it is still a big challenge to unify general relativity and quantum mechanics in modern physics, the theory of quantum field related with the gravitational effect has been well developed and some striking phenomena are predicted, such as Hawking radiation. However, the direct measurement of these quantum effects under general relativity is far beyond present experiment techniques. Fortunately, the emulation of general relativity phenomena in the laboratory has become accessible in recent years. However, up to now, these simulations are limited either in classical regime or in flat space whereas quantum simulation related with general relativity is rarely involved. Here we propose and experimentally demonstrate a quantum evolution of fermions in close proximity to an artificial black hole on a photonic chip. We successfully observe the acceleration behavior, quantum creation, and evolution of a fermion pair near the event horizon: a single-photon wave packet with positive energy escapes from the black hole while negative energy is captured. Our extensible platform not only provides a route to access quantum effects related with general relativity, but also has the potentiality to investigate quantum gravity in future.
Improving photosensitization for photochemical CO2-to-CO conversion
Authors: Wang Ping , Dong Ru , Guo Song , Zhao Jianzhang , Zhang Zhi-Ming , Lu Tong-Bu 
Published: May 2020

Abstract
Inspired by nature, improving photosensitization represents a vital direction for the development of artificial photosynthesis. The sensitization ability of photosensitizers (PSs) reflects in their electron-transfer ability, which highly depends on their excited-state lifetime and redox potential. Herein, for the first time, we put forward a facile strategy to improve sensitizing ability via finely tuning the excited state of Ru(II)-PSs (Ru-1–Ru-4) for efficient CO2 reduction. Remarkably, [Ru(Phen)2(3-pyrenylPhen)]2+ (Ru-3) exhibits the best sensitizing ability among Ru-1–Ru-4, over 17 times higher than that of typical Ru(Phen)32+. It can efficiently sensitize a dinuclear cobalt catalyst for CO2-to-CO conversion with a maximum turnover number of 66 480. Systematic investigations demonstrate that its long-lived excited state and suitable redox driving force greatly contributed to this superior sensitizing ability. This work provides a new insight into dramatically boosting photocatalytic CO2 reduction via improving photosensitization.
Preliminary evidence from a multicenter prospective observational study of the safety and efficacy of chloroquine for the treatment of COVID-19
Authors: Huang Mingxing , Li Man , Xiao Fei , Pang Pengfei , Liang Jiabi , Tang Tiantian , Liu Shaoxuan , Chen Binghui , Shu Jingxian , You Yingying , Li Yang , Tang Meiwen , Zhou Jianhui , Jiang Guanmin , Xiang Jingfen , Hong Wenxin , He Songmei , Wang Zhaoqin , Feng Jianhua , Lin Changqing , Ye Yinong , Wu Zhilong , Li Yaocai , Zhong Bei , Sun Ruilin , Hong Zhongsi , Liu Jing , Chen Huili , Wang Xiaohua , Li Zhonghe , Pei Duanqing , Tian Lin , Xia Jinyu , Jiang Shanping , Zhong Nanshan , Shan Hong 
Published: May 2020

AbstractEffective therapies are urgently needed for the SARS-CoV-2 pandemic. Chloroquine has been proved to have antiviral effect against coronavirus in vitro. In this study, we aimed to assess the efficacy and safety of chloroquine with different doses in COVID-19. In this multicenter prospective observational study, we enrolled patients older than 18 years old with confirmed SARS-CoV-2 infection excluding critical cases from 12 hospitals in Guangdong and Hubei Provinces. Eligible patients received chloroquine phosphate 500 mg, orally, once (half dose) or twice (full dose) daily. Patients treated with non-chloroquine therapy were included as historical controls. The primary endpoint is the time to undetectable viral RNA. Secondary outcomes include the proportion of patients with undetectable viral RNA by day 10 and 14, hospitalization time, duration of fever, and adverse events. A total of 197 patients completed chloroquine treatment, and 176 patients were included as historical controls. The median time to achieve an undetectable viral RNA was shorter in chloroquine than in non-chloroquine (absolute difference in medians −6.0 days; 95% CI −6.0 to −4.0). The duration of fever is shorter in chloroquine (geometric mean ratio 0.6; 95% CI 0.5 to 0.8). No serious adverse events were observed in the chloroquine group. Patients treated with half dose experienced lower rate of adverse events than with full dose. Although randomized trials are needed for further evaluation, this study provides evidence for safety and efficacy of chloroquine in COVID-19 and suggests that chloroquine can be a cost-effective therapy for combating the COVID-19 pandemic.
Previously Derived Host Gene Expression Classifiers Identify Bacterial and Viral Etiologies of Acute Febrile Respiratory Illness in a South Asian Population
Authors: Tillekeratne L Gayani , Suchindran Sunil , Ko Emily R , Petzold Elizabeth A , Bodinayake Champica K , Nagahawatte Ajith , Devasiri Vasantha , Kurukulasooriya Ruvini , Nicholson Bradly P , McClain Micah T , Burke Thomas W , Tsalik Ephraim L , Henao Ricardo , Ginsburg Geoffrey S , Reller Megan E , Woods Christopher W 
Published: May 2020

AbstractBackgroundPathogen-based diagnostics for acute respiratory infection (ARI) have limited ability to detect etiology of illness. We previously showed that peripheral blood-based host gene expression classifiers accurately identify bacterial and viral ARI in cohorts of European and African descent. We determined classifier performance in a South Asian cohort.MethodsPatients ≥15 years with fever and respiratory symptoms were enrolled in Sri Lanka. Comprehensive pathogen-based testing was performed. Peripheral blood ribonucleic acid was sequenced and previously developed signatures were applied: a pan-viral classifier (viral vs nonviral) and an ARI classifier (bacterial vs viral vs noninfectious).ResultsRibonucleic acid sequencing was performed in 79 subjects: 58 viral infections (36 influenza, 22 dengue) and 21 bacterial infections (10 leptospirosis, 11 scrub typhus). The pan-viral classifier had an overall classification accuracy of 95%. The ARI classifier had an overall classification accuracy of 94%, with sensitivity and specificity of 91% and 95%, respectively, for bacterial infection. The sensitivity and specificity of C-reactive protein (&gt;10 mg/L) and procalcitonin (&gt;0.25 ng/mL) for bacterial infection were 100% and 34%, and 100% and 41%, respectively.ConclusionsPreviously derived gene expression classifiers had high predictive accuracy at distinguishing viral and bacterial infection in South Asian patients with ARI caused by typical and atypical pathogens.
Deep Sequencing of Varicella-Zoster Virus in Aqueous Humor From a Patient With Acute Retinal Necrosis Presenting With Acute Glaucoma
Authors: von Hofsten Joanna , Ringlander Johan , Norberg Peter , Zetterberg Madeleine , Andersson Maria , Lindh Magnus , Bergström Tomas 
Published: May 2020

Abstract
We report a case of acute retinal necrosis presenting with acute glaucoma preceding inflammatory signs by several days. High-throughput sequencing on aqueous humor revealed a low-level diversity in the viral genome comparable to diversity seen in cutaneous vesicles in contrast to high diversity in encephalitis.
Hospital Associated Respiratory Virus Infection in Children and Adults: It Does Not Just Occur During Cold and Flu Season
Authors: Petrie Joshua G , Lauring Adam S , Martin Emily T , Kaye Keith S 
Published: May 2020

Abstract
Hospital-associated respiratory virus infections (HARVI) are an underappreciated source of morbidity and mortality. We examined HARVI incidence and clinical respiratory virus testing practices in a cohort of hospitalized patients with acute respiratory illness. HARVI were identified in patients of all ages, both during and outside of the influenza season.