bluuebunny/crossref_metadata_2025_split huggingface dataset:
HECNet: a hierarchical approach to enzyme function classification using a Siamese Triplet Network
Authors: Memon Safyan Aman , Khan Kinaan Aamir , Naveed Hammad 
Published: May 2020

Abstract

Motivation
Understanding an enzyme’s function is one of the most crucial problem domains in computational biology. Enzymes are a key component in all organisms and many industrial processes as they help in fighting diseases and speed up essential chemical reactions. They have wide applications and therefore, the discovery of new enzymatic proteins can accelerate biological research and commercial productivity. Biological experiments, to determine an enzyme’s function, are time-consuming and resource expensive.

Results
In this study, we propose a novel computational approach to predict an enzyme’s function up to the fourth level of the Enzyme Commission (EC) Number. Many studies have attempted to predict an enzyme’s function. Yet, no approach has properly tackled the fourth and final level of the EC number. The fourth level holds great significance as it gives us the most specific information of how an enzyme performs its function. Our method uses innovative deep learning approaches along with an efficient hierarchical classification scheme to predict an enzyme’s precise function. On a dataset of 11 353 enzymes and 402 classes, we achieved a hierarchical accuracy and Macro-F1 score of 91.2% and 81.9%, respectively, on the 4th level. Moreover, our method can be used to predict the function of enzyme isoforms with considerable success. This methodology is broadly applicable for genome-wide prediction that can subsequently lead to automated annotation of enzyme databases and the identification of better/cheaper enzymes for commercial activities.

Availability and implementation
The web-server can be freely accessed at http://hecnet.cbrlab.org/.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Controlled Arena of Contested Practices: Critical Practice in Israel’s State Social Services
Authors: Timor-Shlevin Shachar 
Published: May 2020

AbstractScholars claim that the integration of critical social work into public social services is impossible considering its weak position in the managerialist context of these services. Consequently, critical practice is mainly described as covert and reflective of the hierarchical power dynamics between managerialism and critical professionalism. Thus, the option of integrating critical social work into the institutionalised operation of the profession, which involves engaging in critical practice to the extent possible in the context of public services beyond micro and covert practices, has not been sufficiently described. This study addresses this gap, exploring the process of implementing the critical professional ‘Poverty-Aware Social Work Paradigm’ (PAP) into the Israeli public welfare services. Based on twenty-five interviews with field-level social workers in the PAP programmes, the findings describe critical practices as operating simultaneously at the interpersonal and structural levels, mainly through covert actions. The discussion illustrates the significance of merging the interpersonal and structural levels of critical practice and describes the limited arena in which critical professionalism operates in public services.
Utility of positron emission–computed tomography for predicting pathological response in resectable oesophageal squamous cell carcinoma after neoadjuvant chemoradiation
Authors: Lee Jiyun , Choi Joon Young , Lim Sung Won , Ahn Myung-Ju , Park Keunchil , Zo Jae Il , Shim Young Mog , Oh Dongryul , Sun Jong-Mu 
Published: May 2020

Abstract

OBJECTIVES
For patients with locally advanced oesophageal cancer, improved complete pathological response after neoadjuvant chemoradiation (nCRT) and the detrimental effects on the quality of life related to oesophagectomy have led to the need for a reliable method to select patients who have achieved complete pathological response and do not need surgery. The reliability of 18F-fluorodeoxyglucose positron emission–computed tomography (PET-CT) for predicting the pathological response after nCRT was evaluated.

METHODS
Patients with locally advanced oesophageal cancer who were treated with nCRT and oesophagectomy from July 2010 to February 2017 were analysed. On the post-nCRT PET-CT, a complete metabolic response was defined as all tumourous lesions demonstrating maximum standardized uptake value (SUVmax) ≤2.5. To minimize the effect of radiation-induced oesophagitis, complete metabolic response was also defined as no viable lesion distinguishable from the background with diffuse uptake. The sensitivity, specificity, positive predictive value and negative predictive value were analysed for SUVmax, [X]ΔSUVmax and %ΔSUVmax.

RESULTS
A total of 158 patients with oesophageal squamous cell carcinoma were analysed. The rate of complete pathological response was 27.8%, and that of complete metabolic response was 7.6%. The sensitivity, specificity, positive predictive value and negative predictive value based on SUVmax ≤2.5 and visual normalization were 95%, 14%, 74% and 50%, respectively. Analysis for [X]ΔSUVmax and %ΔSUVmax using the optimal cut-off values determined by the receiver operating characteristic curves did not show an improved predictive efficacy.

CONCLUSIONS
PET-CT is not a reliable tool for predicting pathological response. Patients diagnosed with resectable oesophageal cancer who underwent neoadjuvant therapy should not be exempt from surgery based on PET-CT results.
Functional role of yeasts, lactic acid bacteria and acetic acid bacteria in cocoa fermentation processes
Authors: De Vuyst Luc , Leroy Frédéric 
Published: May 2020

ABSTRACT
Cured cocoa beans are obtained through a post-harvest, batchwise process of fermentation and drying carried out on farms in the equatorial zone. Fermentation of cocoa pulp-bean mass is performed mainly in heaps or boxes. It is made possible by a succession of yeast, lactic acid bacteria (LAB) and acetic acid bacteria (AAB) activities. Yeasts ferment the glucose of the cocoa pulp into ethanol, perform pectinolysis and produce flavour compounds, such as (higher) alcohols, aldehydes, organic acids and esters. LAB ferment the glucose, fructose and citric acid of the cocoa pulp into lactic acid, acetic acid, mannitol and pyruvate, generate a microbiologically stable fermentation environment, provide lactate as carbon source for the indispensable growth of AAB, and contribute to the cocoa and chocolate flavours by the production of sugar alcohols, organic acids, (higher) alcohols and aldehydes. AAB oxidize the ethanol into acetic acid, which penetrates into the bean cotyledons to prevent seed germination. Destruction of the subcellular seed structure in turn initiates enzymatic and non-enzymatic conversions inside the cocoa beans, which provides the necessary colour and flavour precursor molecules (hydrophilic peptides, hydrophobic amino acids and reducing sugars) for later roasting of the cured cocoa beans, the first step of the chocolate-making.
The body-wave magnitude mb: an attempt to rationalize the distance-depth correction q(Δ, h)
Authors: Saloor Nooshin , Okal Emile A 
Published: May 2020

SUMMARYWe explore the possible theoretical origin of the distance–depth correction q(Δ, h) introduced 75 yr ago by B. Gutenberg for the computation of the body-wave magnitude mb, and still in use today. We synthesize a large data set of seismograms using a modern model of P-wave velocity and attenuation, and process them through the exact algorithm mandated under present-day seismological practice, to build our own version, qSO, of the correction, and compare it to the original ones, q45 and q56, proposed by B. Gutenberg and C.F. Richter. While we can reproduce some of the large scale variations in their corrections, we cannot understand their small scale details. We discuss a number of possible sources of bias in the data sets used at the time, and suggest the need for a complete revision of existing mb catalogues.
Simulated Sunlight Rapidly Inactivates SARS-CoV-2 on Surfaces
Authors: Ratnesar-Shumate Shanna , Williams Gregory , Green Brian , Krause Melissa , Holland Brian , Wood Stewart , Bohannon Jordan , Boydston Jeremy , Freeburger Denise , Hooper Idris , Beck Katie , Yeager John , Altamura Louis A , Biryukov Jennifer , Yolitz Jason , Schuit Michael , Wahl Victoria , Hevey Michael , Dabisch Paul 
Published: May 2020

Abstract
Previous studies have demonstrated that SARS-CoV-2 is stable on surfaces for extended periods under indoor conditions. In the present study, simulated sunlight rapidly inactivated SARS-CoV-2 suspended in either simulated saliva or culture media and dried on stainless steel coupons. Ninety percent of infectious virus was inactivated every 6.8 minutes in simulated saliva and every 14.3 minutes in culture media when exposed to simulated sunlight representative of the summer solstice at 40°N latitude at sea level on a clear day. Significant inactivation also occurred, albeit at a slower rate, under lower simulated sunlight levels. The present study provides the first evidence that sunlight may rapidly inactivate SARS-CoV-2 on surfaces, suggesting that persistence, and subsequently exposure risk, may vary significantly between indoor and outdoor environments. Additionally, these data indicate that natural sunlight may be effective as a disinfectant for contaminated nonporous materials.
Serum Procalcitonin Levels Predict Mortality Risk in Patients With Pulmonary Tuberculosis: A Single-Center Prospective Observational Study
Authors: Osawa Takeshi , Watanabe Masato , Morimoto Kozo , Okumura Masao , Yoshiyama Takashi , Ogata Hideo , Goto Hajime , Kudoh Shoji , Ohta Ken , Sasaki Yuka 
Published: May 2020

Abstract
Globally, tuberculosis is the leading infectious cause of death; discovering biomarkers that predict a high mortality risk may improve treatment outcomes. We prospectively enrolled 252 pulmonary tuberculosis patients who were not coinfected with human immunodeficiency virus and initiated antituberculosis treatment, measured serum procalcitonin levels (PCT), and assessed mortality risk. PCT serum levels higher than 0.13 (day 0), 0.05 (day 7), 0.12 (day 14), or 0.06 (day 28) ng/mL predicted nonsurvivors with odds ratios of 7.9, 14.3, 20.0, and 7.3, respectively (P ≤ .005 for all), respectively. Therefore, serum PCT levels are a promising mortality risk indicator for patients with pulmonary tuberculosis.
Main Point. For patients with pulmonary tuberculosis, a promising mortality risk indicator is the level of serum procalcitonin, which is weakly associated with sputum bacterial load and independent of radiographic findings.
COVID-19 and the potential long-term impact on antimicrobial resistance
Authors: Rawson Timothy M , Moore Luke S P , Castro-Sanchez Enrique , Charani Esmita , Davies Frances , Satta Giovanni , Ellington Matthew J , Holmes Alison H 
Published: May 2020

Abstract
The emergence of the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) has required an unprecedented response to control the spread of the infection and protect the most vulnerable within society. Whilst the pandemic has focused society on the threat of emerging infections and hand hygiene, certain infection control and antimicrobial stewardship policies may have to be relaxed. It is unclear whether the unintended consequences of these changes will have a net-positive or -negative impact on rates of antimicrobial resistance. Whilst the urgent focus must be on controlling this pandemic, sustained efforts to address the longer-term global threat of antimicrobial resistance should not be overlooked.
Time-Dependent Changes in THC Concentrations in Deceased Persons
Authors: Chu Mark , Rago Matthew Di , Mantinieks Dylan , Glowacki Linda , Woodford Noel W , Gerostamoulos Dimitri , Drummer Olaf H 
Published: May 2020

Abstract
Changes in the concentrations of Δ9-tetrahydrocannabinol (THC) in the postmortem period were investigated in a series of cases by comparing concentrations in blood taken on receipt of the body in the mortuary (admission specimen, AD) with the concentrations obtained in blood taken at autopsy some time later and also from blood specimens taken antemortem. Overall, the median THC concentration in AD blood was 13.7 ng/mL (n = 239, range LOQ–220), while the median concentration at autopsy was 13.8 ng/mL (n = 106, range LOQ–810) and 1.9 ng/mL (n = 147, range LOQ–48) antemortem. Fourteen cases had all three specimens taken from the same decedent. The corresponding AM, AD and PM median concentrations were 4.0 (range LOQ–48), 15.5 (range 4.0–176) and 4.4 ng/mL (LOQ–56), respectively. The median elapsed times from AM to AD and AD to PM were 33 and 97.5 h, respectively. In contrast, acetaminophen showed no change in blood concentration from AM to AD (6.8 and 6.0 mg/L, respectively). These data show large increases in THC concentration in the early postmortem period, followed by a decline, although the median blood concentrations at autopsy were similar to that obtained antemortem. In contrast, when blood was taken from the femoral region, subclavian and heart ventricles sites, in the same case, the THC concentrations, while variable, showed overall no significant difference. These dynamic changes reflect complex phenomenon occurring in deceased persons and will further serve to increase the uncertainty over any interpretation of postmortem THC concentrations.
UPLC–MS-Based Procedures to Detect Prolyl-Hydroxylase Inhibitors of HIF in Urine
Authors: Mazzarino Monica , Perretti Ilaria , Stacchini Carlotta , Comunità Fabio , de la Torre Xavier , Botrè Francesco 
Published: May 2020

Abstract
This article presents newly developed screening and confirmation analytical procedures to detect the misuse of nine prolyl-hydroxylase inhibitors of the hypoxia-inducible factor: daprodustat, desidustat, FG2216, IOX2, IOX4, JNJ-42041935, molidustat, roxadustat and vadadustat, targeting either the parent drugs and/or their main metabolite(s). For the sample pretreatment, different extraction protocols and technologies were evaluated. The instrumental analysis was performed by ultra-high-performance liquid chromatography coupled to either high- or low-resolution mass spectrometry. The chromatographic separation was performed on a C18 column, employing water and acetonitrile, both containing 0.1% formic acid, as mobile phase. Detection was achieved using as analyzer either a triple quadrupole or an Orbitrap, with positive and negative electrospray ionization and different acquisition modes. Validation of the procedures was performed according to the ISO 17025 and World Anti-Doping Agency guidelines. The methods do not show any significant interference at the retention times of the analytes of interest. The extraction efficiency was estimated to be greater than 75% for all analytes and the matrix effect smaller than 35%. Detection capability was determined in the range of 0.25–2.0 for the screening procedure and in the range of 0.5–2.0 ng/mL for the confirmation procedure, that is, in a range of concentration small enough to reveal the abuse of the compounds considered, in case they are used as performance-enhancing agents. The repeatability of the relative retention times (CV% &lt; 0.5) and of the relative abundances of the selected ion transitions, considered only in the case of triple quadrupole (CV% &lt; 15), was confirmed to be fit for purpose to ensure the unambiguous identification of all the target analytes in human urine. The applicability of the newly developed methods was verified by the analysis of urine samples containing molidustat, roxadustat or daprodustat. The developed procedures enabled to detect the compounds under investigation and their main metabolites.
The Canadian POEM Experience: The First 50 Patients
Authors: Rai Mandip , Woo Matthew , Bechara Robert 
Published: May 2020

Abstract

Background and Aims
Peroral endoscopic myotomy (POEM) has emerged as a less invasive technique for performing myotomy in patients with achalasia. This study aims to assess the safety and efficacy of POEM in a Canadian tertiary care center.

Methods
All consecutive patients who underwent POEM between March 2016 and May 2018 at a tertiary center were included. The primary outcome of the study was clinical success rate of POEM defined as a post-POEM Eckardt score ≤3 at ≥3 months. Adverse events were recorded according to the Clavien-Dindo grading system.

Results
A total of 50 consecutive patients underwent 51 POEM procedures with a mean procedure length of 85.6 ± 29.6 min. Post-POEM Eckardt scores of ≤3 at ≥3 months was achieved in 98% of patients. The incidence of pathologic reflux post-poem was 23%. The median length of hospital stay was 1 day. No major adverse events occurred.

Interpretation
POEM is a safe and effective procedure for the treatment of achalasia. At a median follow-up of 19.5 months, 98% of patients had sustained clinical response (Eckardt score ≤3).
International Investment Agreements, Human Rights, and Environmental Justice: The Texaco/Chevron Case From the Ecuadorian Amazon
Authors: Pellegrini Lorenzo , Arsel Murat , Orta-Martínez Martí , Mena Carlos F 
Published: May 2020

Abstract
The Texaco/Chevron lawsuit, which started in November 1993 and is still being litigated in 2020, is a prominent example of the process of judicialization of environmental conflict. The Ecuadorian plaintiffs claim that the oil company’s operations generated ruinous impacts on the environment and on the development prospects and health of nearby individuals and communities. The tortuous and lengthy judiciary process was further hindered by an arbitration process, an Investor–State Dispute Settlement mechanism nested in the Ecuador—United States Bilateral Investment Treaty. The significance of the case goes beyond the specifics of Ecuador and provides further arguments fuelling the protracted legitimacy crisis experienced by International Investment Agreements. The current praxis of Investor–State Dispute Settlement mechanisms is generating an asymmetrical system, protecting the interest of investors, and intruding into the space of human and environmental rights. These issues are resonating with social movements, activist scholars and policy makers who are reacting to the vulnerabilities engendered by International Investment Agreements through multipronged strategies. These asymmetries provide ammunition to resist the signing of new International Investment Agreements, support the inclusion of human and environmental rights safeguards in International Investment Agreements, and contribute to the rationale of pre-empting extractive projects that are likely to produce severe environmental liabilities. Some of the potential ways in which a somewhat more level playing field can be created include, in addition to denouncing investment agreements, transforming Investor–State Dispute Settlement mechanisms towards a format that can also accommodate the complaints of affected communities or enacting moratoria on extraction projects that are prone to adverse socioenvironmental impacts. Both strategies could prove to be productive avenues towards the achievement of justice.
Bioethics and the Rule of Law: A Classical Liberal Theory
Authors: Brodrick Michael 
Published: May 2020

Abstract
Heated debates over healthcare policy in the United States point to the need for a legal framework that can sustain both moral diversity and peaceful cooperation. It is argued that the classical liberal Rule of Law, with its foundation in the ethical principle of permission, is such a framework. The paper shows to what extent the current healthcare policy landscape in the United States diverges from the rule of law and suggests how the current framework could be modified in order to better approximate that ideal. Two objections are then answered. The first is that the rule of law cannot be realized due to the structure of legislatures. The second objection is that government should guarantee both liberty and all of the necessary conditions of autonomy.
Anterior Lumbar Interbody Fusion (ALIF): Technique Video: 2-Dimensional Operative Video
Authors: Duan Pingguo , Guinn Jeremy M V , Pennicooke Brenton , Mehra Ratnesh N , Chang Chih-Chang , Mayer Rory , Wang Minghao , Eichler Charles , Mummaneni Praveen V , Chou Dean 
Published: May 2020

Abstract
This surgical video demonstrates the technique of an anterior lumbar interbody fusion (ALIF). This video demonstrates the surgical approach, technical nuances of ALIF, and pearls. The main surgical anatomy and approach-related risks are discussed. The video demonstrates the nuances of ALIF, discussing the importance of the release of the disc space to allow for height restoration and lordosis, endplate preparation to enhance arthrodesis, and choice of implant size. The incision is made via a left paramedian approach with a retroperitoneal dissection and mobilization of the vasculature for access to the disc space. The ALIF provides direct access to the ventral surface of the exposed disc, allowing for an incision of the anterior longitudinal ligament, bilateral release of the annulus fibrosus, and access to a large surface area of the vertebral endplate. This anterior access allows for the placement of implants with a greater surface area for fusion, and this facilitates restoration of segmental lordosis, disc height improvement, and foraminal height increase. We have received informed consent from this patient for the video of this case.
Paying by Donating: Corporate Donations Affiliated with Independent Directors
Authors: Cai Ye , Xu Jin , Yang Jun 
Published: May 2020

AbstractCorporate donations to charities affiliated with the board’s independent directors (affiliated donations) are large and mostly undetected due to lack of formal disclosure. Affiliated donations may impair independent directors’ monitoring incentives. CEO compensation is on average 9.4% higher at firms making affiliated donations than at other firms, and it is much higher when the compensation committee chair or a large fraction of compensation committee members are involved. We find suggestive evidence that CEOs are unlikely to be replaced for poor performance when firms donate to charities affiliated with a large fraction of the board or when they donate large amounts.