bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved mutant function prediction via PACT: Protein Analysis and Classifier Toolkit
Authors: Klesmith Justin R , Hackel Benjamin J 
Published: December 2018

Abstract

Motivation
Deep mutational scanning experiments have enabled the measurement of the sequence-function relationship for thousands of mutations in a single experiment. The Protein Analysis and Classifier Toolkit (PACT) is a Python software package that marries the fitness metric of a given mutation within these experiments to sequence and structural features enabling downstream analyses. PACT enables the easy development of user sharable protocols for custom deep mutational scanning experiments as all code is modular and reusable between protocols. Protocols for mutational libraries with single or multiple mutations are included. To exemplify its utility, PACT assessed two deep mutational scanning datasets that measured the tradeoff of enzyme activity and enzyme stability.

Results
PACT efficiently evaluated classifiers that predict protein mutant function tested on deep mutational scanning screens. We found that the classifiers with the lowest false positive and highest true positive rate assesses sequence homology, contact number and if mutation involves proline.

Availability and implementation
PACT and the processed datasets are distributed freely under the terms of the GPL-3 license. The source code is available at GitHub (https://github.com/JKlesmith/PACT).

Supplementary information
Supplementary data are available at Bioinformatics online.
M3Drop: dropout-based feature selection for scRNASeq
Authors: Andrews Tallulah S , Hemberg Martin 
Published: December 2018

Abstract

Motivation
Most genomes contain thousands of genes, but for most functional responses, only a subset of those genes are relevant. To facilitate many single-cell RNASeq (scRNASeq) analyses the set of genes is often reduced through feature selection, i.e. by removing genes only subject to technical noise.

Results
We present M3Drop, an R package that implements popular existing feature selection methods and two novel methods which take advantage of the prevalence of zeros (dropouts) in scRNASeq data to identify features. We show these new methods outperform existing methods on simulated and real datasets.

Availability and implementation
M3Drop is freely available on github as an R package and is compatible with other popular scRNASeq tools: https://github.com/tallulandrews/M3Drop.

Supplementary information
Supplementary data are available at Bioinformatics online.
Asylum Seekers in Israel: Challenges to Social Work
Authors: Nuttman-Shwartz Orit , Shinar Levanon Ofer 
Published: December 2018

AbstractThe challenges facing social workers in addressing the migration crisis are myriad and complex. Against this background, the current article presents a case study on the response of Israeli social work to the asylum seekers, which allows us to identify gaps between the social work profession’s global agenda and its implementation. The article examines how recent immigration policies have impacted Israeli social workers’ responses to these challenges. Following a brief description of Israel’s policies for controlling and limiting the entrance of asylum seekers to the country, the article offers insights into social workers’ involvement in some of the main social services that aim to assist asylum seekers in Israel. Insights are also offered into the response of Israeli social workers to the community of asylum seekers, which focuses on individual needs and on urgent needs. Several explanations for these emphases was offers, noting that they may reflect a more general gap between repeated statements about the significance of human rights for the social work profession on the one hand and the professional reality on the other. Finally, several strategies for social work in the community of asylum seekers and in society as a whole are recommended.
Monopoly capital and entrepreneurship: whither small business?
Authors: Lambert Thomas E 
Published: December 2018

Abstract
There has been a growing body of literature over the last several years on a possible decline in US entrepreneurship and the reasons for it. US small business formation and the jobs created by small businesses are supposed to be key elements in US economic growth. Many claim that without growth in small businesses and the jobs they provide that the US economy will either not grow at all or only very slowly. Therefore, small business is a key to understanding capitalism in the twenty-first century since under monopoly capital, there is claimed to be a tendency towards economic concentration (at the expense of small business) and towards economic stagnation. Some of the general causes mentioned for less US entrepreneurism include high levels of debt among the US populace and the increasing challenges that small businesses face against larger ones. Another concern is the amount of increasing business regulation and government presence in the US economy with which small businesses struggle more than larger ones. If entrepreneurism requires risk taking, then high levels of household debt and large, well-financed potential competitors may be hindering prospective entrepreneurs. This exploratory paper finds that these factors are highly correlated with the slowdown in the entry rates of new firms into the US economy since the late 1970s as well as with a slowdown in the job creation rate of these firms.
Role of conspecifics and personal experience on behavioral avoidance of contaminated flowers by bumblebees
Authors: Fouks Bertrand , Robb Emily G , Lattorff H Michael G 
Published: December 2018

Abstract
Pollinators use multiple cues whilst foraging including direct cues from flowers and indirect cues from other pollinators. The use of indirect social cues is common in social insects, such as honeybees and bumblebees, where a social environment facilitates the ability to use such cues. Bumblebees use cues to forage on flowers according to previous foraging experiences. Flowers are an essential food source for pollinators but also pose a high risk of parasite infection through the shared use of flowers leading to parasite spillover. Nevertheless, bumblebees have evolved behavioral defense mechanisms to limit parasite infection by avoiding contaminated flowers. Mechanisms underlying the avoidance of contaminated flowers by bumblebees are poorly understood. Bumblebees were recorded having the choice to forage on non-contaminated flowers and flowers contaminated by a trypan osome gut parasite, Crithidia bombi. The use of different treatments with presence or absence of conspecifics on both contaminated and non-contaminated flowers allowed to investigate the role of social visual cues on their pathogen avoidance behavior. Bumblebees are expected to use social visual cues to avoid contaminated flowers. Our study reveals that the presence of a conspecific on flowers either contaminated or not does not help bumblebee foragers avoiding contaminated flowers. Nevertheless, bumblebees whereas gaining experience tend to avoid their conspecific when placed on contaminated flower and copy it when on the non-contaminated flower. Our experiment suggests a detrimental impact of floral scent on disease avoidance behavior.
Characterization of functionally significant coronary artery disease by a coronary computed tomography angiography-based index: a comparison with positron emission tomography
Authors: Anagnostopoulos Constantinos D , Siogkas Panagiotis K , Liga Riccardo , Benetos Georgios , Maaniitty Teemu , Sakellarios Antonis I , Koutagiar Iosif , Karakitsios Ioannis , Papafaklis Michail I , Berti Valentina , Sciagrà Roberto , Scholte Arthur J H A , Michalis Lampros K , Gaemperli Oliver , Kaufmann Philipp A , Pelosi Gualtiero , Parodi Oberdan , Knuuti Juhani , Fotiadis Dimitrios I , Neglia Danilo 
Published: December 2018

Abstract

Aims
To test the hypothesis that virtual functional assessment index (vFAI) is related with regional flow parameters derived by quantitative positron emission tomography (PET) and can be used to assess abnormal vasodilating capability in coronary vessels with stenotic lesions at coronary computed tomography angiography (CCTA).

Methods and results
vFAI, stress myocardial blood flow (MBF), and myocardial flow reserve (MFR) were assessed in 78 patients (mean age 62.2 ± 7.7 years) with intermediate pre-test likelihood of coronary artery disease (CAD). Coronary stenoses ≥50% were considered angiographically significant. PET was considered positive for significant CAD, when more than one contiguous segments showed stress MBF ≤2.3 mL/g/min for 15O-water or <1.79 mL/g/min for 13N-ammonia. MFR thresholds were ≤2.5 and ≤2.0, respectively. vFAI was lower in vessels with abnormal stress MBF (0.76 ± 0.10 vs. 0.89 ± 0.07, P < 0.001) or MFR (0.80 ± 0.10 vs. 0.89 ± 0.07, P < 0.001). vFAI had an accuracy of 78.6% and 75% in unmasking abnormal stress MBF and MFR in 15O-water and 82.7% and 71.2% in 13N-ammonia studies, respectively. Addition of vFAI to anatomical CCTA data increased the ability for predicting abnormal stress MBF and MFR in 15O-water studies [AUCccta + vfai = 0.866, 95% confidence interval (CI) 0.783–0.949; P = 0.013 and AUCccta + vfai = 0.737, 95% CI 0.648–0.825; P = 0.007, respectively]. An incremental value was also demonstrated for prediction of stress MBF (AUCccta + vfai = 0.887, 95% CI 0.799–0.974; P = 0.001) in 13N-ammonia studies. A similar trend was recorded for MFR (AUCccta + vfai = 0.780, 95% CI 0.632–0.929; P = 0.13).

Conclusion
vFAI identifies accurately the presence of impaired vasodilating capability. In combination with anatomical data, vFAI enhances the diagnostic performance of CCTA.
Escaped farmed Atlantic salmon in Norwegian rivers during 1989–2013
Authors: Diserud O H , Fiske P , Sægrov H , Urdal K , Aronsen T , Lo H , Barlaup B T , Niemelä E , Orell P , Erkinaro J , Lund R A , Økland F , Østborg G M , Hansen L P , Hindar K 
Published: December 2018

Abstract
We report on the data from an extensive monitoring programme for the occurrence of escaped farmed Atlantic salmon (Salmo salar) in Norwegian rivers for 25 years. This monitoring started as a 3-year research programme in 1989 and was followed by management authorities to cover the proportional occurrence of escaped farmed Atlantic salmon in rivers during summer and autumn before spawning. Farmed salmon were distinguished from wild salmon by growth patterns in the scales. More than 362 000 salmon were registered by this programme. Here we present the historical data on escaped farmed salmon in catches 1989–2013 and a methodology for calculating averages across summer and autumn capture in rivers, across years and in regions, using weighted and unweighted observations. Catches of escaped farmed salmon show large spatial and temporal variation, with the early 1990s and early 2000s being periods of large influxes of farmed fish. Western Norway and parts of middle and northern Norway have shown particularly high incidences of escaped farmed fish. Because escaped farmed Atlantic salmon are competing and interbreeding with wild Atlantic salmon, as well as increasing the spread of disease-causing agents, they have become a major force driving the abundance and evolution of Atlantic salmon.
Replacement, Refinement, and Reduction in Animal Studies With Biohazardous Agents
Authors: Kendall Lon V , Owiny James R , Dohm Erik D , Knapek Katie J , Lee Erin S , Kopanke Jennifer H , Fink Michael , Hansen Sarah A , Ayers Jessica D 
Published: December 2018

Abstract
Animal models are critical to the advancement of our knowledge of infectious disease pathogenesis, diagnostics, therapeutics, and prevention strategies. The use of animal models requires thoughtful consideration for their well-being, as infections can significantly impact the general health of an animal and impair their welfare. Application of the 3Rs—replacement, refinement, and reduction—to animal models using biohazardous agents can improve the scientific merit and animal welfare. Replacement of animal models can use in vitro techniques such as cell culture systems, mathematical models, and engineered tissues or invertebrate animal hosts such as amoeba, worms, fruit flies, and cockroaches. Refinements can use a variety of techniques to more closely monitor the course of disease. These include the use of biomarkers, body temperature, behavioral observations, and clinical scoring systems. Reduction is possible using advanced technologies such as in vivo telemetry and imaging, allowing longitudinal assessment of animals during the course of disease. While there is no single method to universally replace, refine, or reduce animal models, the alternatives and techniques discussed are broadly applicable and they should be considered when infectious disease animal models are developed.
The Modular Adaptive Electrotherapy Delivery System (MAEDS): An Electroceutical Approach for Effective Treatment of Wound Infection and Promotion of Healing
Authors: Bogie Kath M 
Published: December 2018

Abstract

Background
Infected wounds are painful and cannot heal, with antibiotics showing reduced efficacy. Appropriate wound electrotherapy may limit incident planktonic and polymicrobial colonization, inhibit biofilm formation and accelerate healing.

Methods
The Modular Adaptive Electrotherapy Delivery System (MAEDS) is a lightweight, flexible, battery-powered disposable bandage which delivers controlled reliable electrotherapy to the wound for up to 7 days. Large full-thickness excisional wounds (6 cm diameter) were created in a porcine model and freshly cultured 0.5 McFarland green fluorescent protein-labeled Pseudomonas aeruginosa evenly applied to the wound bed. Control wounds received standard wound care, Tegaderm HP Transparent Dressing (3 M Health Care, St. Paul, MN, USA) applied in a sterile fashion. Treatment wounds received MAEDS electrotherapy for up to 28 days or until healed. Onboard Bluetooth facilitated remote real-time monitoring of MAEDS function. Dressing changes occurred on postoperative day (POD) 1, 3, 5, 7, 10, 14, 21, and 28. Punch biopsies were taken at the wound margin and center. Bacterial samples were processed to determine infection status.

Results
Acute infected wounds treated with MAEDS electrotherapy were 92% smaller than baseline by POD21. Healing rate was significantly faster (p &lt; 0.01) and infection significantly decreased (p &lt; 0.0001) at POD10, relative to control wounds.

Conclusion
The MAEDS electrotherapy can significantly inhibit infection and enhance healing rate in acute infected wounds.
QUIJOTE scientific results – III. Microwave spectrum of intensity and polarization in the Taurus Molecular Cloud complex and L1527
Authors: Poidevin F , Rubiño-Martín J A , Dickinson C , Génova-Santos R , Harper S , Rebolo R , Casaponsa B , Peláez-Santos A , Vignaga R , Guidi F , Ruiz-Granados B , Tramonte D , Vansyngel F , Ashdown M , Herranz D , Hoyland R , Lasenby A , Martínez-González E , Piccirillo L , Watson R A 
Published: December 2018

Abstract
We present new intensity and polarization observations of the Taurus Molecular Cloud (TMC) region in the frequency range 10–20 GHz with the multifrequency instrument (MFI) mounted on the first telescope of the Q-U-I-JOint TEnerife (QUIJOTE) experiment. From the combination of the QUIJOTE data with the WMAP 9-yr data release, the Planck second data release, the DIRBE maps, and ancillary data, we detect an anomalous microwave emission (AME) component with flux density $S_{\rm AME, peak} = 43.0 \pm 7.9\,$ Jy in the TMC and $S_{\rm AME, peak} = 10.7 \pm 2.7\,$ Jy in the dark cloud nebula L1527, which is part of the TMC. In the TMC the diffuse AME emission peaks around a frequency of 19 GHz, compared with an emission peak about a frequency of 25 GHz in L1527. In the TMC, the best constraint on the level of AME polarization is obtained at the Planck channel of 28.4 GHz, with an upper limit $\pi _{\rm AME}\lt 4.2\, {{\ \rm per\ cent}}$ (95 $\, {{\ \rm per\ cent}}$ C.L.), which reduces to $\pi _{\rm AME}\lt 3.8\, {{\ \rm per\ cent}}$ (95 $\, {{\ \rm per\ cent}}$ C.L.) if the intensity of all the free–free, synchrotron and thermal dust components are negligible at this frequency. The same analysis in L1527 leads to $\pi _{\rm AME}\lt 5.3{{\ \rm per\ cent}}$ (95 $\, {{\ \rm per\ cent}}$ C.L.) or $\pi _{\rm AME}\lt 4.5\, {{\ \rm per\ cent}}$ (95 ${{\ \rm per\ cent}}$ C.L.) under the same assumption. We find that in the TMC and L1527 on average about $80{{\ \rm per\ cent}}$ of the H ii gas should be mixed with thermal dust. Our analysis shows how the QUIJOTE-MFI 10–20 GHz data provide key information to properly separate the synchrotron, free–free, and AME components.
Effect of Prenatal Smoke Exposure on Birth Weight: The Moderating Role of Maternal Depressive Symptoms
Authors: Schechter Julia , Do Elizabeth K , Zhang Junfeng (Jim) , Hoyo Cathrine , Murphy Susan K , Kollins Scott H , Fuemmeler Bernard 
Published: December 2018

AbstractIntroductionBoth prenatal smoke exposure and depression have been linked to lower birth weight, a risk factor for morbidity and mortality. Few studies have looked at the interaction between these risk factors and none have used a biomarker to objectively measure prenatal smoke exposure. The current study sought to examine independent and interactive effects of cotinine and depression on birth weight. The effect of race was also explored.MethodData were drawn from a prospective study of pregnant women (N = 568) in the southeastern United States. Maternal demographic, health information, depressive symptoms, and birth data were collected via self-report and medical record abstraction. Prenatal blood samples were assayed for cotinine.ResultsControlling for covariates, multiple regression analyses indicated that both cotinine and depressive symptoms independently predicted lower birth weight and a significant interaction was also observed. Upon probing the interaction, a negative association between cotinine levels and birth weight was found in the context of higher depression but not lower depression scores. Similarly, logistic regression analyses revealed a significant interaction between cotinine and depression, such that cotinine predicted having a baby less than 2500 g among women who fell above the indicated cutoff score. African American women had the highest levels of cotinine and lowest weight babies; however, race was not a significant moderator.ConclusionsResults suggest prenatal smoke exposure has a greater negative effect on birth weight for women endorsing co-occurring depressive symptoms. Findings can inform targeted interventions and assist medical providers with identifying women at increased risk for poor perinatal outcomes.ImplicationsDespite the common occurrence of smoking during pregnancy and prenatal depression, the interaction between these risk factors on birth weight has rarely been examined. Further, the extant results have been mixed, likely due in part to difficulties in measurement. The current study was the first to use prenatal cotinine to assess bias-free, continuous levels of prenatal smoke exposure. Results indicate that prenatal cotinine was a significant predictor of birth weight only in the context of maternal depressive symptoms. These findings have important implications for mitigating negative perinatal outcomes for pregnant women and their children.
Validation of Apolipoprotein A-1 and Fibronectin Fragments as Markers of Parasitological Cure for Congenital Chagas Disease in Children Treated With Benznidazole
Authors: Ruiz-Lancheros Elizabeth , Rasoolizadeh Asieh , Chatelain Eric , Garcia-Bournissen Facundo , Moroni Samanta , Moscatelli Guillermo , Altcheh Jaime , Ndao Momar 
Published: December 2018

Abstract

Background
No reliable tests or validated biomarkers exist to ensure parasitological cure following treatment of Chagas disease (CD) patients chronically infected with Trypanosoma cruzi. As seroreversion, the only marker of cure, happens more quickly in children, we investigated the correlation between previously identified biomarkers and seroreversion in children.

Methods
Thirty CD children (age 1 month to 10 years) diagnosed as T. cruzi positive (time point S0) were treated with benznidazole (BZ) 5–8 mg/kg/d for 60 days. At least 2 serological tests were used to evaluate treatment efficacy from the end of treatment (S1) until seroreversion (S2). Thirty children (age 1 month to 10 years) and 15 adults were used as healthy controls (HCs). Immunoblot and a proteomic-based assay were used to validate previously identified fragments of apolipoprotein A-1 (ApoA1) and fibronectin (FBN) as CD biomarkers.

Results
Correlation between seroreversion and absence of ApoA1 and FBN fragments by immunoblot was observed in 30/30 (100%) and 29/30 (96.6%) CD children, respectively. ApoA1 and FBN fragments were absent at the end of BZ treatment in 20/30 (66.6%) and 16/30 (53.3%) children, respectively. Absence of fragments in serum profiles was confirmed by mass spectrometry. Using intact protein analysis, a 28 109-Da protein identified as full-length ApoA1 by tandem mass spectrometry was detected in HC serum samples.

Conclusions
These data confirm that ApoA1 and FBN fragments can discriminate between healthy and T. cruzi–infected samples. Correlation with seroreversion was shown for the first time; results suggest predictive capacity potentially superior to serology, making them potentially useful as surrogate biomarkers.
Benefit of Echocardiography in Patients With Staphylococcus aureus Bacteremia at Low Risk of Endocarditis
Authors: Heriot George S , Tong Steven Y C , Cheng Allen C , Liew Danny 
Published: December 2018

Abstract

Background
The risk of endocarditis among patients with Staphylococcus aureus bacteremia is not uniform, and a number of different scores have been developed to identify patients whose risk is less than 5%. The optimal echocardiography strategy for these patients is uncertain.

Methods
We used decision analysis and Monte Carlo simulation using input parameters taken from the existing literature. The model examined patients with S aureus bacteremia whose risk of endocarditis is less than 5%, generally those with nosocomial or healthcare-acquired bacteremia, no intracardiac prosthetic devices, and a brief duration of bacteremia. We examined 6 echocardiography strategies, including the use of transesophageal echocardiography, transthoracic echocardiography, both modalities, and neither. The outcome of the model was 90-day survival.

Results
The optimal echocardiography strategy varied with the risk of endocarditis and the procedural mortality associated with transesophageal echocardiography. No echocardiography strategy offered an absolute benefit in 90-day survival of more than 0.5% compared with the strategy of not performing echocardiography and treating with short-course therapy. Strategies using transesophageal echocardiography were never preferred if the mortality of this procedure was greater than 0.5%.

Conclusions
In patients identified to be at low risk of endocarditis, the choice of echocardiography strategy appears to exert a very small influence on 90-day survival. This finding may render test-treatment trials unfeasible and should prompt clinicians to focus on other, more important, management considerations in these patients.
Timing and mode of intervention for patients with left sided valvular heart disease: an individualized approach
Authors: McConkey Hannah , Zhao Zhengang , Redwood S , Chen M , Prendergast B D 
Published: December 2018

Abstract
Left sided valvular heart disease poses major impact on life and lifestyle. Medical therapy merely palliates chronic severe valve disease and once symptoms or haemodynamic sequelae appear, life expectancy is markedly truncated. In this article, we review the mechanisms of valve pathology, latest evidence in the quest for pharmacological options, means by which to predict deterioration, and standard and novel treatment options.