bluuebunny/crossref_metadata_2025_split huggingface dataset:
Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach
Authors: Guil Francisco , Hidalgo José F , García José M 
Published: April 2020

Abstract

Motivation
Elementary flux modes (EFMs) are a key tool for analyzing genome-scale metabolic networks, and several methods have been proposed to compute them. Among them, those based on solving linear programming (LP) problems are known to be very efficient if the main interest lies in computing large enough sets of EFMs.

Results
Here, we propose a new method called EFM-Ta that boosts the efficiency rate by analyzing the information provided by the LP solver. We base our method on a further study of the final tableau of the simplex method. By performing additional elementary steps and avoiding trivial solutions consisting of two cycles, we obtain many more EFMs for each LP problem posed, improving the efficiency rate of previously proposed methods by more than one order of magnitude.

Availability and implementation
Software is freely available at https://github.com/biogacop/Boost_LP_EFM.

Contact
fguil@um.es

Supplementary information
Supplementary data are available at Bioinformatics online.
The Motor Cortex Has Independent Representations for Ipsilateral and Contralateral Arm Movements But Correlated Representations for Grasping
Authors: Downey John E , Quick Kristin M , Schwed Nathaniel , Weiss Jeffrey M , Wittenberg George F , Boninger Michael L , Collinger Jennifer L 
Published: April 2020

Abstract
Motor commands for the arm and hand generally arise from the contralateral motor cortex, where most of the relevant corticospinal tract originates. However, the ipsilateral motor cortex shows activity related to arm movement despite the lack of direct connections. The extent to which the activity related to ipsilateral movement is independent from that related to contralateral movement is unclear based on conflicting conclusions in prior work. Here we investigate bilateral arm and hand movement tasks completed by two human subjects with intracortical microelectrode arrays implanted in the left hand and arm area of the motor cortex. Neural activity was recorded while they attempted to perform arm and hand movements in a virtual environment. This enabled us to quantify the strength and independence of motor cortical activity related to continuous movements of each arm. We also investigated the subjects’ ability to control both arms through a brain–computer interface. Through a number of experiments, we found that ipsilateral arm movement was represented independently of, but more weakly than, contralateral arm movement. However, the representation of grasping was correlated between the two hands. This difference between hand and arm representation was unexpected and poses new questions about the different ways the motor cortex controls the hands and arms.
High Rates of Recurrent Tuberculosis Disease: A Population-level Cohort Study
Authors: Hermans Sabine M , Zinyakatira Nesbert , Caldwell Judy , Cobelens Frank G J , Boulle Andrew , Wood Robin 
Published: April 2020

Abstract

Background
Retreatment tuberculosis (TB) disease is common in high-prevalence settings. The risk of repeated episodes of recurrent TB is unknown. We calculated the rate of recurrent TB per subsequent episode by matching individual treatment episodes over a period of 13 years.

Methods
All recorded TB episodes in Cape Town between 2003 and 2016 were matched by probabilistic linkage of personal identifiers. Among individuals with a first episode notified in Cape Town and who completed their prior treatment successfully we estimated the recurrence rate stratified by subsequent episode and HIV status. We adjusted person-time to background mortality by age, sex, and HIV status.

Results
A total of 292 915 TB episodes among 263 848 individuals were included. The rate of recurrent TB was 16.4 per 1000 person-years (95% CI, 16.2–16.6), and increased per subsequent episode (8.4-fold increase, from 14.6 to 122.7 per 1000 from episode 2 to 6, respectively). These increases were similar stratified by HIV status. Rates among HIV positives were higher than among HIV negatives for episodes 2 and 3 (2- and 1.5-fold higher, respectively), and the same thereafter.

Conclusions
TB recurrence rates were high and increased per subsequent episode, independent of HIV status. This suggests that HIV infection is insufficient to explain the high burden of recurrence; it is more likely due to a high annual risk of infection combined with an increased risk of infection or progression to disease associated with a previous TB episode. The very high recurrence rates would justify increased TB surveillance of patients with &gt;1 episode.
Methodological Considerations for Cost of Illness Studies of Enteric Fever
Authors: Mejia Nelly , Ramani Enusa , Pallas Sarah W , Song Dayoung , Abimbola Taiwo , Mogasale Vittal 
Published: April 2020

AbstractThis article presents a selection of practical issues, questions, and tradeoffs in methodological choices to consider when conducting a cost of illness (COI) study on enteric fever in low- to lower-middle-income countries. The experiences presented are based on 2 large-scale COI studies embedded within the Surveillance for Enteric Fever in Asia Project II (SEAP II), in Bangladesh, Nepal, and Pakistan; and the Severe Typhoid Fever Surveillance in Africa (SETA) Program in Burkina Faso, Ethiopia, Ghana, and Madagascar. Issues presented include study design choices such as controlling for background patient morbidity and healthcare costs, time points for follow-up, data collection methods for sensitive income and spending information, estimating enteric fever–specific health facility cost information, and analytic approaches in combining patient and health facility costs. The article highlights the potential tradeoffs in time, budget, and precision of results to assist those commissioning, conducting, and interpreting enteric fever COI studies.
HotSpotAnnotations—a database for hotspot mutations and annotations in cancer
Authors: Trevino Victor 
Published: April 2020

Abstract
Hotspots, recurrently mutated DNA positions in cancer, are thought to be oncogenic drivers because random chance is unlikely and the knowledge of clear examples of oncogenic hotspots in genes like BRAF, IDH1, KRAS and NRAS among many other genes. Hotspots are attractive because provide opportunities for biomedical research and novel treatments. Nevertheless, recent evidence, such as DNA hairpins for APOBEC3A, suggests that a considerable fraction of hotspots seem to be passengers rather than drivers. To document hotspots, the database HotSpotsAnnotations is proposed. For this, a statistical model was implemented to detect putative hotspots, which was applied to TCGA cancer datasets covering 33 cancer types, 10 182 patients and 3 175 929 mutations. Then, genes and hotspots were annotated by two published methods (APOBEC3A hairpins and dN/dS ratio) that may inform and warn researchers about possible false functional hotspots. Moreover, manual annotation from users can be added and shared. From the 23 198 detected as possible hotspots, 4435 were selected after false discovery rate correction and minimum mutation count. From these, 305 were annotated as likely for APOBEC3A whereas 442 were annotated as unlikely. To date, this is the first database dedicated to annotating hotspots for possible false functional hotspots.
Population- and Species-Based Variation of Webworm–Parasitoid Interactions in Hogweeds (Heracelum spp.) in the Netherlands
Authors: Harvey Jeffrey A , Ode Paul J , Gols Rieta 
Published: April 2020

Abstract
In three Dutch populations of the native small hogweed (Heracleum sphondylium L. [Apiales: Apiaceae]), and one of the invasive giant hogweed (H. mantegazzianum Sommeier & Levier [Apiales: Apiaceae]), interactions between a specialist herbivore, the parsnip webworm (Depressaria radiella), and its associated parasitoids were compared during a single growing season. We found host plant species-related differences in the abundance of moth pupae, the specialist polyembryonic endoparasitoid, Copidosoma sosares, the specialist pupal parasitoid, Barichneumon heracliana, and a potential hyperparasitoid of C. sosares, Tyndaricus scaurus Walker (Hymenoptera: Encyrtidae). Adult D. radiella body mass was similar across the three small hogweed populations, but moths and their pupal parasitoid B. heracliana were smaller when developing on giant than on small hogweeds where the two plants grew in the same locality (Heteren). Mixed-sex and all-male broods of C. sosares were generally bigger than all-female broods. Furthermore, adult female C. sosares were larger than males and adult female mass differed among the three small hogweed populations. The frequency of pupal parasitism and hyperparasitism also varied in the different H. sphondylium populations. These results show that short-term (intra-seasonal) effects of plant population on multitrophic insects are variable among different species in a tightly linked food chain.
The EACVI survey on cardiac imaging in cardio-oncology
Authors: Stankovic Ivan , Dweck Marc R , Marsan Nina Ajmone , Bergler-Klein Jutta , Holte Espen , Manka Robert , Schulz-Menger Jeanette , Sitges Marta , Haugaa Kristina H 
Published: April 2020

Abstract
Early and late cardiovascular (CV) toxicities related to many cancer treatments may complicate the clinical course of patients, offsetting therapeutic benefits, and altering prognosis. The early detection, monitoring, and treatment of cardiotoxicity have therefore become essential parts of cancer patient care. CV imaging is a cornerstone of every cardio-oncology unit, but its use may vary across Europe because of the non-uniform availability of advanced imaging techniques and differences in the organization and logistics of cardio-oncology services. The purpose of this EACVI survey in cardio-oncology is to obtain real-world data on the current usage of cardiac imaging in cancer patients. Data from 104 centres and 35 different countries confirmed that cardiac imaging plays a pivotal role in the detection and monitoring of cardiac toxicity in oncology patients in Europe and beyond. However, it also revealed gaps between guidelines recommendations and everyday clinical practice, highlighting some of the challenges that need to be overcome in this rapidly advancing field.
New expectations for diastolic function assessment in transthoracic echocardiography based on a semi-automated computing of strain–volume loops
Authors: Hubert Arnaud , Le Rolle Virginie , Galli Elena , Bidaud Auriane , Hernandez Alfredo , Donal Erwan 
Published: April 2020

Abstract

Aims
Early diagnosis of heart failure with preserved ejection fraction (HFpEF) by determination of diastolic dysfunction is challenging. Strain–volume loop (SVL) is a new tool to analyse left ventricular function. We propose a new semi-automated method to calculate SVL area and explore the added value of this index for diastolic function assessment.

Method and results
Fifty patients (25 amyloidosis, 25 HFpEF) were included in the study and compared with 25 healthy control subjects. Left ventricular ejection fraction was preserved and similar between groups. Classical indices of diastolic function were pathological in HFpEF and amyloidosis groups with greater left atrial volume index, greater mitral average E/e’ ratio, faster tricuspid regurgitation (P &lt; 0.0001 compared with controls). SVL analysis demonstrated a significant difference of the global area between groups, with the smaller area in amyloidosis group, the greater in controls and a mid-range value in HFpEF group (37 vs. 120 vs. 72 mL.%, respectively, P &lt; 0.0001). Applying a linear discriminant analysis (LDA) classifier, results show a mean area under the curve of 0.91 for the comparison between HFpEF and amyloidosis groups.

Conclusion
SVLs area is efficient to identify patients with a diastolic dysfunction. This new semi-automated tool is very promising for future development of automated diagnosis with machine-learning algorithms.
Handgrip Strength Asymmetry and Weakness Together Are Associated With Functional Disability in Aging Americans
Authors: McGrath Ryan , Vincent Brenda M , Jurivich Donald A , Hackney Kyle J , Tomkinson Grant R , Dahl Lindsey J , Clark Brian C 
Published: April 2020

Abstract

Background
Evaluating handgrip strength (HGS) asymmetry may help to improve the prognostic value of HGS. This study sought to determine the associations of HGS asymmetry and weakness on future activities of daily living (ADL) disability in a national sample of aging Americans.

Methods
The analytic sample included 18,468 Americans aged ≥50 years from the 2006–2016 waves of the Health and Retirement Study. A handgrip dynamometer measured HGS. Those with HGS &gt;10% stronger on either hand were considered as having any HGS asymmetry. Individuals with HGS &gt;10% stronger on their dominant hand were considered as having dominant HGS asymmetry, while those with HGS &gt;10% stronger on their nondominant hand were classified as having nondominant HGS asymmetry. Men with HGS &lt;26 kg and women with HGS &lt;16 kg were considered weak. ADLs were self-reported. Generalized estimating equations were used for analyses.

Results
Relative to those with symmetric HGS and no weakness, each HGS asymmetry and weakness group had increased odds for future ADL disability: 1.11 (95% confidence interval [CI]: 1.02–1.20) for any HGS asymmetry alone, 1.42 (CI: 1.16–1.74) for weakness alone, and 1.81 (CI: 1.52–2.16) for both any HGS asymmetry and weakness. Most weakness and HGS asymmetry dominance groups had increased odds for future ADL disability: 1.30 (CI: 1.13–1.50) for nondominant HGS asymmetry alone, 1.42 (CI: 1.16–1.74) for weakness alone, 1.72 (CI: 1.29–2.29) for both weakness and nondominant HGS asymmetry, and 1.86 (CI: 1.52–2.28) for both weakness and dominant HGS asymmetry.

Conclusions
HGS asymmetry and weakness together may increase the predictive utility of handgrip dynamometers.
2-D multiparameter viscoelastic shallow-seismic full-waveform inversion: reconstruction tests and first field-data application
Authors: Gao Lingli , Pan Yudi , Bohlen Thomas 
Published: April 2020

SUMMARY
2-D full-waveform inversion (FWI) of shallow-seismic wavefields has recently become a novel way to reconstruct S-wave velocity models of the shallow subsurface with high vertical and lateral resolution. In most applications, seismic wave attenuation is ignored or considered as a passive modelling parameter only. In this study, we explore the feasibility and performance of multiparameter viscoelastic 2-D FWI in which seismic velocities and attenuation of P and S waves, respectively, and mass density are inverted simultaneously. Synthetic reconstruction experiments reveal that multiple crosstalks between all viscoelastic material parameters may occur. The reconstruction of S-wave velocity is always robust and of high quality. The parameters P-wave velocity and density exhibit weaker sensitivity and can be reconstructed more reliably by multiparameter viscoelastic FWI. Anomalies in S-wave attenuation can be recovered but with limited resolution. In a field-data application, a small-scale refilled trench is nicely delineated as a low P- and S-wave velocity anomaly. The reconstruction of P-wave velocity is improved by the simultaneous inversion of attenuation. The reconstructed S-wave attenuation reveals higher attenuation in the shallow weathering zone and weaker attenuation below. The variations in the reconstructed P- and S-wave velocity models are consistent with the reflectivity observed in a ground penetrating radar (GPR) profile.
Fourier Coefficients of Modular Forms of Half-Integral Weight in Arithmetic Progressions
Authors: Darreye Corentin 
Published: April 2020

Abstract
We study the probabilistic behavior of sums of Fourier coefficients in arithmetic progressions. We prove a result analogous to previous work of Fouvry–Ganguly–Kowalski–Michel and Kowalski–Ricotta in the context of half-integral weight holomorphic cusp forms and for prime power modulus. We actually show that these sums follow in a suitable range a mixed Gaussian distribution that comes from the asymptotic mixed distribution of Salié sums.
Epidemiological Characteristics and Incubation Period of 7015 Confirmed Cases With Coronavirus Disease 2019 Outside Hubei Province in China
Authors: Nie Xiuquan , Fan Lieyang , Mu Ge , Tan Qiyou , Wang Mengyi , Xie Yujia , Cao Limin , Zhou Min , Zhang Zhuang , Chen Weihong 
Published: April 2020

Abstract

Background
Disease caused by SARS-CoV-2 broke out in Wuhan in December 2019. We utilized confirmed cases outside Hubei Province to analyze epidemiologic characteristics and evaluate the effect of traffic restrictions implemented in Hubei beginning on 23 January 2020.

Methods
Information on 7015 confirmed cases from 19 January to 8 February 2020 in all provinces outside Hubei was collected from the national and local health commissions in China. Incubation period and interval times were calculated using dates of the following events: contact with an infected person, onset, first visit, and diagnosis. We evaluated changes in incubation period and interval times.

Results
The average age of all cases was 44.24 years. The median incubation period was 5 days and extended from 2 days on 23 January to 15 days on 8 February. The proportion of imported cases decreased from 85.71% to 33.19% after 23 January. In addition, lengths of intervals between onset and diagnosis, onset and first visit, and first visit and diagnosis decreased over time.

Conclusions
Rapidly transmitting COVID-19 has a short incubation period. The onset mainly occurred among young to middle-aged adults. Traffic restrictions played an important role in the decreased number of imported cases outside Hubei.
The Militarized Interstate Dispute Dataset: Putting Things in Perspective
Authors: Palmer Glenn , D'Orazio Vito , Kenwick Michael R , McManus Roseanne W 
Published: April 2020

Abstract
In their latest research note in our ongoing dialogue about the Militarized Interstate Dispute (MID) dataset, Gibler, Miller, and Little (GML) reiterate their concerns about a high error rate in the MID dataset and challenge our prior replication studies, which showed that GML's recommended changes to the dataset caused few substantive changes in the core findings of two published studies. In this rejoinder, we offer further explanation of our decision-making, put GML's claims about the error rate in context, defend our replication methodology and results, and offer advice for MID dataset users.
Efficacy and safety of selective decontamination of the digestive tract (SDD) to prevent recurrent hepatic cyst infections in polycystic liver disease: a retrospective case series
Authors: Bernts Lucas H P , Dekker Shosha E I , Soonawala Darius , Brüggemann Roger J M , Wertheim Heiman F L , de Fijter Johan W , Drenth Joost P H , Lantinga Marten A 
Published: April 2020

Abstract

Background
Hepatic cyst infection is a complication of polycystic liver disease (PLD) that causes substantial morbidity. Repetitive infection is frequent and is increasingly difficult to treat. As translocated gut bacteria are considered the cause, we hypothesize that selective decontamination of the digestive tract (SDD) reduces recurrence of hepatic cyst infection.

Methods
We performed a retrospective, observational study in two referral centres. All patients with PLD treated with SDD for hepatic cyst infection were included. Efficacy was determined by calculating the infection incidence (hepatic cyst infections per month) before and during SDD therapy. Adverse events were scored according to the Common Terminology Criteria for Adverse Events (CTCAE).

Results
We identified eight patients who received SDD (88% female, 88% polycystic kidney disease). The median age was 65 years (IQR: 51–74 years). SDD lowered the median incidence from 0.09 episodes per month (IQR: 0.06–0.25 episodes per month) to 0.01 episodes per month (IQR: 0.00–0.05 episodes per month) (P = 0.12). Discontinuation of SDD led to rapid recurrence of cyst infection (71% within 6 weeks). SDD consisted of polymyxins with/without aminoglycosides. The median SDD treatment duration was 20 months (range: 3–89 months). Six patients (75%) developed adverse events [CTCAE Grade 1 (gastrointestinal: n = 3) or Grade 3 (ototoxicity: n = 1; fungal infection: n = 1)], mostly attributable to aminoglycosides; one patient developed polymyxin E resistance.

Conclusions
SDD prophylaxis provides a novel strategy for limiting recurrent hepatic cyst infection in PLD patients. However, adverse events are frequent and curtail its use. As most were attributable to aminoglycosides, polymyxin E is considered the preferred therapy.
Dalbavancin for the management of osteomyelitis: a major step forward?
Authors: Almangour Thamer A , Alhifany Abdullah A 
Published: April 2020

AbstractOsteomyelitis is one of the most challenging infectious diseases to treat and is associated with a significant burden to healthcare systems. There are limited available therapeutic options to treat osteomyelitis caused by Gram-positive pathogens and these are not without limitations. Dalbavancin is a long-acting lipoglycopeptide, approved for the treatment of acute bacterial skin and skin structure infections caused by designated susceptible strains of Gram-positive microorganisms. It demonstrated promising pharmacokinetic/pharmacodynamic properties and safety data to be considered for the treatment of bone infections. However, information on the effectiveness and safety of dalbavancin in the treatment of invasive Gram-positive infections, such as osteomyelitis, is very limited. In this review, we describe the novel characteristics and potential utility of dalbavancin in the treatment of osteomyelitis and summarize its long-term clinical outcomes from published case reports, series and comparative studies.
Preoperative Wire Localization of the Breast on the Day Before Surgery
Authors: Sanders Linda M , Morgan Dina , Polini Nicole , Mehta Avani 
Published: April 2020

Abstract

Objective
To assess the feasibility and accuracy of preoperative wire localization performed one day prior to surgery and the relationship between the time interval following wire placement with migration distance within the time-window examined.

Methods
Two trials were performed with next-day mammography to assess migration. Trial 1 used a standard hooked wire (50 patients, 61 wires). Trial 2 employed a looped wire (50 patients, 59 wires). A third trial was subsequently performed (16 patients, 18 wires) using the looped wire without repeat mammograms. Complications were recorded. Comparative statistical analyses were performed between patients in Trial 1 and Trial 2.

Results
In Trials 1 and 2, no wires required readjustment on the day of surgery. Mean and maximum migration were less with the looped wire (range: 0–7 mm) compared to the hooked wire (range: 0–18 mm), allowing for the elimination of next-day mammograms in Trial 3. A Mann–Whitney U test showed no significant difference between the migration distances for the first two trials (P = 0.11). A Chi-square test showed no significant difference in the direction of the migration between the two trials (P = 0.15). There was no correlation between the time interval of localization and needle migration in the first two trials (r = -0.16, P = 0.22 and -0.12, P = 0.36). Specimen radiographs demonstrated the lesion/biopsy marker clip in all cases in all three trials. No infections or bleeding occurred. Two patients developed an allergic reaction to adhesive.

Conclusion
Wire localization performed on the day before surgery is feasible, inexpensive, did not compromise accuracy, and successfully unlinked the radiologic and surgical procedures.