bluuebunny/crossref_metadata_2025_split huggingface dataset:
ClonArch: visualizing the spatial clonal architecture of tumors
Authors: Wu Jiaqi , El-Kebir Mohammed 
Published: May 2020

Abstract

Motivation
Cancer is caused by the accumulation of somatic mutations that lead to the formation of distinct populations of cells, called clones. The resulting clonal architecture is the main cause of relapse and resistance to treatment. With decreasing costs in DNA sequencing technology, rich cancer genomics datasets with many spatial sequencing samples are becoming increasingly available, enabling the inference of high-resolution tumor clones and prevalences across different spatial coordinates. While temporal and phylogenetic aspects of tumor evolution, such as clonal evolution over time and clonal response to treatment, are commonly visualized in various clonal evolution diagrams, visual analytics methods that reveal the spatial clonal architecture are missing.

Results
This article introduces ClonArch, a web-based tool to interactively visualize the phylogenetic tree and spatial distribution of clones in a single tumor mass. ClonArch uses the marching squares algorithm to draw closed boundaries representing the presence of clones in a real or simulated tumor. ClonArch enables researchers to examine the spatial clonal architecture of a subset of relevant mutations at different prevalence thresholds and across multiple phylogenetic trees. In addition to simulated tumors with varying number of biopsies, we demonstrate the use of ClonArch on a hepatocellular carcinoma tumor with ∼280 sequencing biopsies. ClonArch provides an automated way to interactively examine the spatial clonal architecture of a tumor, facilitating clinical and biological interpretations of the spatial aspects of intra-tumor heterogeneity.

Availability and implementation
https://github.com/elkebir-group/ClonArch.
Chloroquine Inhibits the Release of Inflammatory Cytokines by Human Lung Explants
Authors: Grassin-Delyle Stanislas , Salvator Hélène , Brollo Marion , Catherinot Emilie , Sage Edouard , Couderc Louis-Jean , Naline Emmanuel , Devillier Philippe 
Published: May 2020

Abstract
On human lung parenchymal explants, chloroquine concentration clinically achievable in the lung (100 µM) inhibited the lipopolysaccharide-induced release of TNF-ɑ (by 76%), IL-6 (by 68%), CCL2 (by 72%), and CCL3 (by 67%). Besides its antiviral activity, chloroquine might also mitigate the cytokine storm associated with severe pneumonia caused by coronaviruses.
Why data citation isn't working, and what to do about it
Authors: Buneman Peter , Christie Greig , Davies Jamie A , Dimitrellou Roza , Harding Simon D , Pawson Adam J , Sharman Joanna L , Wu Yinjun 
Published: May 2020

Abstract
We describe a system that automatically generates from a curated database a collection of short conventional publications—citation summaries—that describe the contents of various components of the database. The purpose of these summaries is to ensure that the contributors to the database receive appropriate credit through the currently used measures such as h-indexes. Moreover, these summaries also serve to give credit to publications and people that are cited by the database. In doing this, we need to deal with granularity—how many summaries should be generated to represent effectively the contributions to a database? We also need to deal with evolution—for how long can a given summary serve as an appropriate reference when the database is evolving? We describe a journal specifically tailored to contain these citation summaries. We also briefly discuss the limitations that the current mechanisms for recording citations place on both the process and value of data citation.
The Effect of Gender-Targeted Conditional Cash Transfers on Household Expenditures: Evidence from a Randomized Experiment
Authors: Armand Alex , Attanasio Orazio , Carneiro Pedro , Lechene Valérie 
Published: May 2020

Abstract
This article studies the differential effect of targeting cash transfers to men or women on household expenditure on non-durables. We study a policy intervention in the Republic of North Macedonia that offers cash transfers to poor households, conditional on having their children attending secondary school. The recipient is randomised across municipalities, with payments targeted to either the mother or the father of the child. Targeting transfers to women increases the expenditure share on food by 4 to 5 percentage points. At low levels of food expenditure, there is a shift towards a more nutritious diet.
The effect of a primary care-based Medical Weight Loss Program on weight loss and anthropomorphic metrics
Authors: Rose Vivienne A , Klyushnenkova Elena N , Zhang Min , Warrington Verlyn O 
Published: May 2020

Abstract

Background
Diet and lifestyle intervention programs have been shown to be effective in decreasing obesity/overweight and many associated comorbidities in specialty research settings. There is very little information however as to the efficacy of such programs conducted in usual/typical primary care practices. We analysed effectiveness of the Medical Weight Loss Program (MWLP) designed to specifically address overweight/obesity in the setting of an urban academic primary care practice.

Objective
To determine whether participation in the MWLP within a general primary care setting can result in weight loss.

Methods
A retrospective medical chart review of patients treated in MWLP and a control group of patients with obesity receiving regular care in the general primary care setting. From the practice database (1 April 2015–31 March 2016), 209 patients (≥18 years old) who participated in the MWLP were identified; 265 controls were selected from the remaining population based on the presence of the obesity-related diagnoses.

Results
MWLP patients lost on average 2.35 ± 5.88 kg in 6 months compared to their baseline weight (P &lt; 0.0001). In contrast, the control group demonstrated a trend of gaining on average 0.37 ± 6.03 kg. Having three or more visits with the MWLP provider within 6 months after program initiation was the most important factor associated with successful loss of at least 5% of the baseline weight. Weight loss also correlated with a decrease in abdominal girth.

Conclusion
MWLP integrated into the general primary care practice may potentially be an effective model for managing obesity and related morbidities.
Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle
Authors: Lim Suk-Kyung , Kim Dongjun , Moon Dong-Chan , Cho Youna , Rho Mina 
Published: May 2020

Abstract

Background
Antibiotics administered to farm animals have led to increasing prevalence of resistance genes in different microbiomes and environments. While antibiotic treatments help cure infectious diseases in farm animals, the possibility of spreading antibiotic resistance genes into the environment and human microbiomes raises significant concerns. Through long-term evolution, antibiotic resistance genes have mutated, thereby complicating the resistance problems.

Results
In this study, we performed deep sequencing of the gut microbiomes of 36 swine and 41 cattle in Korean farms, and metagenomic analysis to understand the diversity and prevalence of antibiotic resistance genes. We found that aminoglycoside, β-lactam, lincosamide, streptogramin, and tetracycline were the prevalent resistance determinants in both swine and cattle. Tetracycline resistance was abundant and prevalent in cattle and swine. Specifically, tetQ, tetW, tetO, tet32, and tet44 were the 5 most abundant and prevalent tetracycline resistance genes. Their prevalence was almost 100% in swine and cattle. While tetQ was similarly abundant in both swine and cattle, tetW was more abundant in swine than in cattle. Aminoglycoside was the second highest abundant resistance determinant in swine, but not in cattle. In particular, ANT(6) and APH(3′′) were the dominant resistance gene families in swine. β-lactam was also an abundant resistance determinant in both swine and cattle. Cfx was the major contributing gene family conferring resistance against β-lactams.

Conclusions
Antibiotic resistome was more pervasive in swine than in cattle. Specifically, prevalent antibiotic resistance genes (prevalence &gt;50%) were found more in swine than in cattle. Genomic investigation of specific resistance genes from the gut microbiomes of swine and cattle in this study should provide opportunities to better understand the exchange of antibiotic resistance genes in farm animals.
Utilizing pre-polarization to enhance SNMR signals—effect of imperfect switch-off
Authors: Hiller Thomas , Dlugosch Raphael , Müller-Petke Mike 
Published: May 2020

SUMMARYSurface nuclear magnetic resonance (SNMR) is a well-established technique for the hydrogeological characterization of the subsurface up to depths of about 150 m. Recently, SNMR has been adapted to investigate also the shallow unsaturated zone with small surface loop setups. Due to the decreased volume, a pre-polarization (PP) field prior to the classical spin excitation is applied to enhance the measured response signal. Depending on the strength and orientation of the applied PP-field, the enhancement can often reach several orders of magnitude in the vicinity of the PP-loop. The theoretically achievable enhancement depends on the assumption of an adiabatic, that is perfect, switch-off of the corresponding PP-field. To study the effect of imperfect switch-off, we incorporate full spin dynamics simulations into the SNMR forward modelling. The affected subsurface volume strongly depends on the chosen PP switch-off ramp and the geometry of the loop setup. Due to the imperfect switch-off, the resulting SNMR sounding curves can have significantly decreased signal amplitudes. For comparison, the signal amplitudes of either a 1 ms exponential or linear switch-off ramp are reduced by 17 and 65 per cent, respectively. Disregarding this effect would therefore yield an underestimation of the corresponding subsurface water content of similar magnitude.
Methods for the robust computation of the long-period seismic spectrum of broad-band arrays
Authors: Caton Ross C , Pavlis Gary L , Thomson David J , Vernon Frank L 
Published: May 2020

SUMMARY
We describe array methods to search for low signal-to-noise ratio (SNR) signals in long-period seismic data using Fourier analysis. This is motivated by published results that find evidence of solar free oscillations in the Earth's seismic hum. Previous work used data from only one station. In this paper, we describe methods for computing spectra from array data. Arrays reduce noise level through averaging and provide redundancy that we use to distinguish coherent signal from a random background. We describe two algorithms for calculating a robust spectrum from seismic arrays, an algorithm that automatically removes impulsive transient signals from data, a jackknife method for estimating the variance of the spectrum, and a method for assessing the significance of an entire spectral band. We show examples of their application to data recorded by the Homestake Mine 3-D array in Lead, SD and the Piñon Flats PY array. These are two of the quietest small aperture arrays ever deployed in North America. The underground Homestake data has exceptionally low noise, and the borehole sensors of the PY array also have very low noise, making these arrays well suited to finding very weak signals. We find that our methods remove transient signals effectively from the data so that even low-SNR signals in the seismic background can be found and tested. Additionally, we find that the jackknife variance estimate is comparable to the noise floor, and we present initial evidence for solar g-modes in our data through the T2 test, a multivariate generalization of Student's t-test.
Strategies used to establish palliative care in rural low- and middle-income countries: an integrative review
Authors: Aregay Atsede , O’Connor Margaret , Stow Jill , Ayers Nicola , Lee Susan 
Published: May 2020

Abstract
Globally, 40 million people need palliative care; about 69% are people over 60 years of age. The highest proportion (78%) of adults are from low- and middle-income countries (LMICs), where palliative care still developing and is primarily limited to urban areas. This integrative review describes strategies used by LMICs to establish palliative care in rural areas. A rigorous integrative review methodology was utilized using four electronic databases (Ovid MEDLINE, Ovid Emcare, Embase classic+Embase and CINAHL). The search terms were: ‘palliative care’, ‘hospice care’, ‘end of life care’, ‘home-based care’, ‘volunteer’, ‘rural’, ‘regional’, ‘remote’ and ‘developing countries’ identified by the United Nations (UN) as ‘Africa’, ‘Sub-Saharan Africa’, ‘low-income’ and ‘middle- income countries’. Thirty papers published in English from 1990 to 2019 were included. Papers were appraised for quality and extracted data subjected to analysis using a public health model (policy, drug availability, education and implementation) as a framework to describe strategies for establishing palliative care in rural areas. The methodological quality of the reviewed papers was low, with 7 of the 30 being simple programme descriptions. Despite the inclusion of palliative care in national health policy in some countries, implementation in the community was often reliant on advocacy and financial support from non-government organizations. Networking to coordinate care and medication availability near-patient homes were essential features of implementation. Training, role play, education and mentorship were strategies used to support health providers and volunteers. Home- and community-based palliative care services for rural LMICs communities may best be delivered using a networked service among health professionals, community volunteers, religious leaders and technology.
Circulating Rather Than Alveolar Extracellular Deoxyribonucleic Acid Levels Predict Outcomes in Influenza
Authors: Zhang Nannan , Zhu Liuluan , Zhang Yue , Zhou Chun , Song Rui , Yang Xiaoyu , Huang Linna , Xiong Shuyu , Huang Xu , Xu Fei , Wang Yajie , Wan Gang , Chen Zhihai , Li Ang , Zhan Qingyuan , Zeng Hui 
Published: May 2020

Abstract

Background
High levels of circulating neutrophil extracellular traps (NETs) are associated with a poor prognosis in influenza A infection. It remains unclear whether NETs in the plasma or bronchoalveolar lavage fluid (BALF) can predict clinical outcomes in influenza.

Methods
One hundred eighteen patients who were diagnosed with H1N1 influenza in 2017–2018 were recruited. The NETs were assessed in plasma and BALF samples by quantifying cell-free deoxyribonucleic acid (cfDNA) and protein-DNA complexes. Predictions of severe illness and 60-day mortality were analyzed with receiver operating characteristic curves.

Results
The NET levels were significantly elevated in the BALF and contributed to the pathology of lungs, yet it was not associated with disease severity or mortality in patients severely infected with H1N1. Plasma NET levels were significantly increased in the patients with severe influenza and positively correlated with the oxygen index and sequential organ failure assessment scores. High levels of plasma cfDNA (&gt;286.6 ng/mL) or histone-bound DNA (&gt;9.4 ng/mL) discriminated severe influenza from mild, and even higher levels of cfDNA (&gt;306.3 ng/mL) or histone-bound DNA (&gt;23.1 ng/mL) predicted fatal outcomes in severely ill patients.

Conclusions
The cfDNA and histone-bound DNA in plasma represent early predictive biomarkers for the prognosis of influenza.
Physical Function Impairment and Frailty in Middle-Aged People Living With Human Immunodeficiency Virus in the REPRIEVE Trial Ancillary Study PREPARE
Authors: Umbleja Triin , Brown Todd T , Overton Edgar T , Ribaudo Heather J , Schrack Jennifer A , Fitch Kathleen V , Douglas Pamela S , Grinspoon Steven K , Henn Sarah , Arduino Roberto C , Rodriguez Benigno , Benson Constance A , Erlandson Kristine M 
Published: May 2020

AbstractBackgroundPeople with human immunodeficiency virus (PWH) are at risk for accelerated development of physical function impairment and frailty; both associated with increased risk of falls, hospitalizations, and death. Identifying factors associated with physical function impairment and frailty can help target interventions.MethodsThe REPRIEVE trial enrolled participants 40–75 years of age, receiving stable antiretroviral therapy with CD4+ T-cell count &gt;100 cells/mm3, and with low to moderate cardiovascular disease risk. We conducted a cross-sectional analysis of those concurrently enrolled in the ancillary study PREPARE at enrollment.ResultsAmong the 266 participants, the median age was 51 years; 81% were male, and 45% were black, and 28% had hypertension. Body mass index (BMI; calculated as weight in kilograms divided by height in meters squared) was 25 to &lt;30 in 38% and ≥30 in 30%, 33% had a high waist circumference, 89% were physically inactive, 37% (95% confidence interval, 31%, 43%) had physical function impairment (Short Physical Performance Battery score ≤10), and 6% (4%, 9%) were frail and 42% prefrail. In the adjusted analyses, older age, black race, greater BMI, and physical inactivity were associated with physical function impairment; depression and hypertension were associated with frailty or prefrailty.ConclusionsPhysical function impairment was common among middle-aged PWH; greater BMI and physical inactivity are important modifiable factors that may prevent further decline in physical function with aging.Clinical Trials RegistrationNCT02344290.
Lineage-Specific Expansion of Plasmodium falciparum Parasites With pfhrp2 Deletion in the Greater Mekong Subregion
Authors: Gibbons Justin , Qin Junling , Malla Pallavi , Wang Zenglei , Brashear Awtum , Wang Chengqi , Miao Jun , Adams John H , Kim Kami , Jiang Rays , Cui Liwang 
Published: May 2020

Abstract
Deletion of the pfhrp2 gene in Plasmodium falciparum can lead to false-negative rapid diagnostic test (RDT) results, constituting a major challenge for evidence-based malaria treatment. Here we analyzed the whole genome sequences of 138 P. falciparum clinical samples collected from the China-Myanmar boarder for pfhrp2 and pfhrp3 gene deletions. We found pfhrp2 and pfhrp3 deletions in 9.4% and 3.6% of samples, respectively, with no samples harboring deletions of both genes. The pfhrp2 deletions showed 2 distinct breakpoints, representing 2 different chromosomal deletion events. A phylogenetic analysis performed using genome-wide single-nucleotide polymorphisms revealed that the 2 pfhrp2 breakpoint groups as well as all the pfhrp3-negative parasites formed separate clades, suggesting they might have resulted from clonal expansion of pfhrp2- and pfhrp3-negative parasites. These findings highlight the need for urgent surveys to determine the prevalence of pfhrp2-negative parasites causing false-negative RDT results and a plan for switching of RDTs pending the survey results.
High-Throughput Screening of Kawasaki Disease Sera for Antiviral Antibodies
Authors: Quiat Daniel , Kula Tomasz , Shimizu Chisato , Kanegaye John T , Tremoulet Adriana H , Pitkowsky Zachary , Son MaryBeth , Newburger Jane W , Elledge Stephen J , Burns Jane C 
Published: May 2020

Abstract
Clinical features of Kawasaki disease (KD) display overlap with common pediatric viral illnesses, leading some to hypothesize that a viral infection is the inciting event for KD. To investigate viral infection history in KD patients, we performed comprehensive serological profiling using a high-throughput phage immunoprecipitation sequencing assay covering the complete reference protein sequences of known viruses with human tropism. KD and matched febrile control sera did not demonstrate differences in antiviral antibody profiles. We conclude that in the acute and subacute phases of disease, KD patients do not exhibit serologic evidence of exposure to known viruses that differs from controls.
Characterization of AmpC-hyperproducing Escherichia coli from humans and dairy farms collected in parallel in the same geographical region
Authors: Alzayn Maryam , Findlay Jacqueline , Schubert Hannah , Mounsey Oliver , Gould Virginia C , Heesom Kate J , Turner Katy M , Barrett David C , Reyher Kristen K , Avison Matthew B 
Published: May 2020

AbstractObjectivesTo characterize putative AmpC-hyperproducing third-generation cephalosporin-resistant E. coli from dairy farms and their phylogenetic relationships; to identify risk factors for their presence; and to assess evidence for their zoonotic transmission into the local human population.MethodsProteomics was used to explain differences in antimicrobial susceptibility. WGS allowed phylogenetic analysis. Multilevel, multivariable logistic regression modelling was used to identify risk factors.ResultsIncreased use of amoxicillin/clavulanate was associated with an increased risk of finding AmpC hyperproducers on farms. Expansion of cephalosporin resistance in AmpC hyperproducers was seen in farm isolates with marR mutations (conferring cefoperazone resistance) or when AmpC was mutated (conferring fourth-generation cephalosporin and cefoperazone resistance). Phylogenetic analysis confirmed the dominance of ST88 amongst farm AmpC hyperproducers but there was no evidence for acquisition of farm isolates by members of the local human population.ConclusionsClear evidence was found for recent farm-to-farm transmission of AmpC-hyperproducing E. coli and of adaptive mutations to expand resistance. Whilst there was no evidence of isolates entering the local human population, efforts to reduce third-generation cephalosporin resistance on dairy farms must address the high prevalence of AmpC hyperproducers. The finding that amoxicillin/clavulanate use was associated with an increased risk of finding AmpC hyperproducers is important because this is not currently categorized as a highest-priority critically important antimicrobial and so is not currently targeted for specific usage restrictions in the UK.
Identification of Proteus genomic island 2 variants in two clonal Proteus mirabilis isolates with coexistence of a novel genomic resistance island PmGRI1
Authors: Lei Chang-Wei , Yao Tian-Ge , Yan Jia , Li Bo-Yang , Wang Xue-Chun , Zhang Yu , Gao Yu-Feng , Wang Hong-Ning 
Published: May 2020

AbstractObjectivesTo characterize the MDR genomic islands (GIs) in Proteus mirabilis isolates.MethodsTwo P. mirabilis strains (C55 and C74) of chicken origin were subjected to WGS (HiSeq and PacBio) and the MDR GIs were determined.ResultsP. mirabilis strains C55 and C74 are clonal strains and harbour different Proteus genomic island 2 (PGI2) variants (PGI2-C55 and PGI2-C74). The MDR region of PGI2-C55 is composed of two class 1 integrons, separated by a region containing seven copies of IS26 and eight resistance genes, including blaCTX-M-3 and fosA3. The region in PGI2-C74 is a complete In4-type class 1 integron, harbouring five gene cassettes (dfrA16, blaCARB-2, aadA2, cmlA1 and aadA1). In addition, C55 and C74 carry an SXT/R391 integrative and conjugative element (ICEPmiJpn1), harbouring blaCMY-2, and a novel 50.46 kb genomic resistance island named PmGRI1-C55. PmGRI1-C55 harbours a tyrosine-type recombinase/integrase that might be responsible for the integration of PmGRI1-C55 at the 3′ end of tRNA-Sec. It carries an MDR region derived from Tn2670 that harbours a Tn21 region and carries six resistance genes (catA1, blaTEM-1b, aphA1a, sul2, strA and strB). Blast analysis showed diverse PmGRI1 variants in P. mirabilis and Escherichia coli strains.ConclusionsThe finding of the two new PGI2 variants highlights that the homologous recombination between shared components of class 1 integrons and transposition by IS26 promote the diversity of MDR regions in PGI2. PmGRI1 is a new GI that carries various resistance genes identified in P. mirabilis and E. coli.