bluuebunny/crossref_metadata_2025_split huggingface dataset:
Planning sustainable environmental neighborhoods is a step towards the direction of sustainable cities
Authors: Khalifa Mohammed Ali Nada , Abbas Ahmed Zainab 
Published: April 2021

Abstract
The sustainable environmental neighborhoods is sustainable development of neighborhoods that include considerations related to transport, density, urban forms, and environmental buildings and especially those related to social and functional integration, and civil society participation, This standard, which did not attract the attention of specialists in the 1990s, has today become a center of attention for all those interested in urbanism and sustainability. The problem of the research is the existence of urban problems in residential neighborhoods that lead to lack of sustainability in the city, and the research aims to explain the role and importance of environmental sustainability of residential neighborhoods in achieving city sustainability assuming that environmental sustainability of residential neighborhoods leads to the sustainability of the city, and as a general methodology for the research, the descriptive analytical method was adopted. The research included sustainable environmental neighborhoods, neighborhood definition, and definition of sustainable neighborhoods, characteristics of sustainable neighborhoods, types of sustainable neighborhoods, goals and standards for sustainable neighborhoods, Sweden’s experience, and the research reached the following main conclusions:
1 - Sustainable environmental neighborhoods are modern neighborhoods that appeared most often in industrial sites that suffer from pollution to give a positive image of these sites to be new neighborhoods that enjoy social, participatory, economic and environmental quality and they are urban poles characterized by density and interconnection and respond to the principle of sustainability in terms of general quality.
2 - The achievement of sustainable neighborhoods is one of the stages towards achieving sustainable cities because it is a test of the principles and directions before achieving the sustainable city.
3 - There are common characteristics of sustainable neighborhoods, including density, functional integration, sustainable transportation, the high quality of the perimeter, intergenerational and social inclusion, prosperity, ease of communication, and control of values and community participation.
Loss of Methylthioadenosine Phosphorylase by Immunohistochemistry Is Common in Pulmonary Sarcomatoid Carcinoma and Sarcomatoid Mesothelioma
Authors: Terra Simone , Roden Anja C , Yi Eunhee S , Aubry Marie Christine , Boland Jennifer M 
Published: April 2021

Abstract

Objectives
Differentiating malignant pleural mesothelioma from benign reactive mesothelial processes can be quite challenging. Ancillary tests such as BRCA1-associated protein 1 (BAP1) immunohistochemistry and p16 fluorescence in situ hybridization (FISH) are helpful tools to aid in this distinction. Immunohistochemistry for methylthioadenosine phosphorylase (MTAP) has recently been proposed as an effective surrogate marker for p16 FISH and is an attractive alternative test due to shorter turnaround time. There are little data regarding the specificity of MTAP loss for mesothelioma or whether it may be useful to distinguish mesothelioma from the most common entity in the differential diagnosis, sarcomatoid carcinoma.

Methods
We studied well-characterized cases of sarcomatoid carcinoma (n = 34) and sarcomatoid mesothelioma (n = 62), which were stained for MTAP (clone 2G4) and BAP1 (clone C-4).

Results
Loss of MTAP expression was observed in 17 (50%) of 34 pulmonary sarcomatoid carcinomas; BAP1 expression was retained in all of the cases in which it was performed (n = 31). MTAP expression was lost in 38 (61%) of 62 sarcomatoid mesotheliomas; BAP1 was lost in 6 (10%) of 62. In the six cases with BAP1 loss, five also had loss of MTAP, while MTAP expression was retained in one.

Conclusions
Loss of MTAP expression by immunohistochemistry is common in pulmonary sarcomatoid carcinoma, as it is present in half of cases. This rate is similar to what is observed in sarcomatoid mesothelioma (61%). Therefore, this stain is not useful to distinguish between these two malignancies. MTAP loss is more common than BAP1 loss in the setting of sarcomatoid mesothelioma (61% vs 10%, respectively).
MS2Planner: improved fragmentation spectra coverage in untargeted mass spectrometry by iterative optimized data acquisition
Authors: Zuo Zeyuan , Cao Liu , Nothia Louis-Félix , Mohimani Hosein 
Published: April 2021

AbstractMotivationUntargeted mass spectrometry experiments enable the profiling of metabolites in complex biological samples. The collected fragmentation spectra are the metabolite’s fingerprints that are used for molecule identification and discovery. Two main mass spectrometry strategies exist for the collection of fragmentation spectra: data-dependent acquisition (DDA) and data-independent acquisition (DIA). In the DIA strategy, all the metabolites ions in predefined mass-to-charge ratio ranges are co-isolated and co-fragmented, resulting in multiplexed fragmentation spectra that are challenging to annotate. In contrast, in the DDA strategy, fragmentation spectra are dynamically and specifically collected for the most abundant ions observed, causing redundancy and sub-optimal fragmentation spectra collection. Yet, DDA results in less multiplexed fragmentation spectra that can be readily annotated.ResultsWe introduce the MS2Planner workflow, an Iterative Optimized Data Acquisition strategy that optimizes the number of high-quality fragmentation spectra over multiple experimental acquisitions using topological sorting. Our results showed that MS2Planner increases the annotation rate by 38.6% and is 62.5% more sensitive and 9.4% more specific compared to DDA.Availability and implementationMS2Planner code is available at https://github.com/mohimanilab/MS2Planner. The generation of the inclusion list from MS2Planner was performed with python scripts available at https://github.com/lfnothias/IODA_MS.Supplementary informationSupplementary data are available at Bioinformatics online.
Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model
Authors: Hosoda Shion , Fukunaga Tsukasa , Hamada Michiaki 
Published: April 2021

Abstract

Motivation
Accumulating evidence has highlighted the importance of microbial interaction networks. Methods have been developed for estimating microbial interaction networks, of which the generalized Lotka–Volterra equation (gLVE)-based method can estimate a directed interaction network. The previous gLVE-based method for estimating microbial interaction networks did not consider time-varying interactions.

Results
In this study, we developed unsupervised learning-based microbial interaction inference method using Bayesian estimation (Umibato), a method for estimating time-varying microbial interactions. The Umibato algorithm comprises Gaussian process regression (GPR) and a new Bayesian probabilistic model, the continuous-time regression hidden Markov model (CTRHMM). Growth rates are estimated by GPR, and interaction networks are estimated by CTRHMM. CTRHMM can estimate time-varying interaction networks using interaction states, which are defined as hidden variables. Umibato outperformed the existing methods on synthetic datasets. In addition, it yielded reasonable estimations in experiments on a mouse gut microbiota dataset, thus providing novel insights into the relationship between consumed diets and the gut microbiota.

Availability and implementation
The C++ and python source codes of the Umibato software are available at https://github.com/shion-h/Umibato.

Supplementary information
Supplementary data are available at Bioinformatics online.
Model learning to identify systemic regulators of the peripheral circadian clock
Authors: Martinelli Julien , Dulong Sandrine , Li Xiao-Mei , Teboul Michèle , Soliman Sylvain , Lévi Francis , Fages François , Ballesta Annabelle 
Published: April 2021

Abstract

Motivation
Personalized medicine aims at providing patient-tailored therapeutics based on multi-type data toward improved treatment outcomes. Chronotherapy that consists in adapting drug administration to the patient’s circadian rhythms may be improved by such approach. Recent clinical studies demonstrated large variability in patients’ circadian coordination and optimal drug timing. Consequently, new eHealth platforms allow the monitoring of circadian biomarkers in individual patients through wearable technologies (rest-activity, body temperature), blood or salivary samples (melatonin, cortisol) and daily questionnaires (food intake, symptoms). A current clinical challenge involves designing a methodology predicting from circadian biomarkers the patient peripheral circadian clocks and associated optimal drug timing. The mammalian circadian timing system being largely conserved between mouse and humans yet with phase opposition, the study was developed using available mouse datasets.

Results
We investigated at the molecular scale the influence of systemic regulators (e.g. temperature, hormones) on peripheral clocks, through a model learning approach involving systems biology models based on ordinary differential equations. Using as prior knowledge our existing circadian clock model, we derived an approximation for the action of systemic regulators on the expression of three core-clock genes: Bmal1, Per2 and Rev-Erbα. These time profiles were then fitted with a population of models, based on linear regression. Best models involved a modulation of either Bmal1 or Per2 transcription most likely by temperature or nutrient exposure cycles. This agreed with biological knowledge on temperature-dependent control of Per2 transcription. The strengths of systemic regulations were found to be significantly different according to mouse sex and genetic background.

Availability and implementation
https://gitlab.inria.fr/julmarti/model-learning-mb21eccb.

Supplementary information
Supplementary data are available at Bioinformatics online.
SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning
Authors: Singh Jaspreet , Litfin Thomas , Paliwal Kuldip , Singh Jaswinder , Hanumanthappa Anil Kumar , Zhou Yaoqi 
Published: April 2021

Abstract

Motivation
Knowing protein secondary and other one-dimensional structural properties are essential for accurate protein structure and function prediction. As a result, many methods have been developed for predicting these one-dimensional structural properties. However, most methods relied on evolutionary information that may not exist for many proteins due to a lack of sequence homologs. Moreover, it is computationally intensive for obtaining evolutionary information as the library of protein sequences continues to expand exponentially. Here, we developed a new single-sequence method called SPOT-1D-Single based on a large training dataset of 39 120 proteins deposited prior to 2016 and an ensemble of hybrid long-short-term-memory bidirectional neural network and convolutional neural network.

Results
We showed that SPOT-1D-Single consistently improves over SPIDER3-Single and ProteinUnet for secondary structure, solvent accessibility, contact number and backbone angles prediction for all seven independent test sets (TEST2018, SPOT-2016, SPOT-2016-HQ, SPOT-2018, SPOT-2018-HQ, CASP12 and CASP13 free-modeling targets). For example, the predicted three-state secondary structure’s accuracy ranges from 72.12% to 74.28% by SPOT-1D-Single, compared to 69.1–72.6% by SPIDER3-Single and 70.6–73% by ProteinUnet. SPOT-1D-Single also predicts SS3 and SS8 with 6.24% and 6.98% better accuracy than SPOT-1D on SPOT-2018 proteins with no homologs (Neff = 1), respectively. The new method’s improvement over existing techniques is due to a larger training set combined with ensembled learning.

Availability and implementation
Standalone-version of SPOT-1D-Single is available at https://github.com/jas-preet/SPOT-1D-Single. Direct prediction can also be made at https://sparks-lab.org/server/spot-1d-single. The datasets used in this research can also be downloaded from GitHub.

Supplementary information
Supplementary data are available at Bioinformatics online.
Impact of Immunosuppressive Agents on Clinical Manifestations and Outcome of Staphylococcus aureus Bloodstream Infection: A Propensity Score–Matched Analysis in 2 Large, Prospectively Evaluated Cohorts
Authors: Camp Johannes , Glaubitz Lina , Filla Tim , Kaasch Achim J , Fuchs Frieder , Scarborough Matt , Kim Hong Bin , Tilley Robert , Liao Chun-Hsing , Edgeworth Jonathan , Nsutebu Emmanuel , López-Cortés Luis Eduardo , Morata Laura , Llewelyn Martin , Fowler Vance G , Thwaites Guy , Seifert Harald , Kern Winfried V , Kuss Oliver , Rieg Siegbert 
Published: April 2021

Abstract

Background
Staphylococcus aureus bloodstream infection (SAB) is a common, life-threatening infection. The impact of immunosuppressive agents on the outcome of patients with SAB is incompletely understood.

Methods
Data from 2 large prospective, international, multicenter cohort studies (Invasive Staphylococcus aureus Infections Cohort [INSTINCT] and International Staphylococcus aureus Collaboration [ISAC]) between 2006 and 2015 were analyzed. Patients receiving immunosuppressive agents were identified and a 1:1 propensity score–matched analysis was performed to adjust for baseline characteristics of patients. Overall survival and time to SAB-related late complications (SAB relapse, infective endocarditis, osteomyelitis, or other deep-seated manifestations) were analyzed by Cox regression and competing risk analyses, respectively. This approach was then repeated for specific immunosuppressive agents (corticosteroid monotherapy and immunosuppressive agents other than steroids [IMOTS]).

Results
Of 3188 analyzed patients, 309 were receiving immunosuppressive treatment according to our definitions and were matched to 309 nonimmunosuppressed patients. After propensity score matching, baseline characteristics were well balanced. In the Cox regression analysis, we observed no significant difference in survival between the 2 groups (death during follow-up: 105/309 [33.9%] immunosuppressed vs 94/309 [30.4%] nonimmunosuppressed; hazard ratio [HR], 1.20 [95% confidence interval {CI}, .84–1.71]). Competing risk analysis showed a cause-specific HR of 1.81 (95% CI, .85–3.87) for SAB-related late complications in patients receiving immunosuppressive agents. The cause-specific HR was higher in patients taking IMOTS (3.69 [95% CI, 1.41–9.68]).

Conclusions
Immunosuppressive agents were not associated with an overall higher mortality. The risk for SAB-related late complications in patients receiving specific immunosuppressive agents such as IMOTS warrants further investigations.
Vasoplegia induces high energy demand and depletes cardiac energetics: a new insight into physiological concepts of cardiac work and a model for acute heart failure?
Authors: Watson W , Neubauer S , Rider OJ 
Published: April 2021

Abstract

Funding Acknowledgements
Type of funding sources: Other. Main funding source(s): British Heart Foundation
Background / Introduction
Hearts subjected to constant high workload will, over time, fail. We hypothesized vasoplegia would create a high cardiac energy demand and deplete cardiac energy reserves, a mechanism causing failure. With 31Phosphorus Magnetic Resonance Spectroscopy, we can measure energy: ATP usage (via creatine kinase flux) and reserves of phosphocreatine (PCr/ATP ratio).

Methods: Ten healthy volunteers were recruited
mean age 37, mean BMI 22.4, 5 male, 5 female. A nitrate vasodilator (Glyceryl trinitrate, GTN) was used to induce vasoplegia, with MRI and MRS measurements taken before and during.

Results
There was reduced preload (falls in end diastolic volume and right atrial area) and afterload (mean blood pressure fall 14mmHg, p &lt;0.0001). Subjects mounted reflex tachycardia (mean heart rate rise 9bpm, p &lt; 0.0001) and inotropy (mean baseline ejection fraction increase 5%, p = 0.0002) hence cardiac output and rate pressure product were maintained (baseline CO 6.24 ± 1.45 L/min vs GTN 6.49 ± 1.43 L/min, p = 0.37; baseline RPP = 6929 ± 976 mmHg.bpm vs GTN 7214 ± 1051 mmHg.bpm, p = 0.06).
There was a 58% increase in Creatine Kinase activity (kf) (baseline 0.158 s-1 vs GTN 0.249 s-1, p = 0.006) and CK flux (baseline 1.79 ± 0.78 umol/g/s vs GTN 2.59 ± 1.07 umol/g/s, p = 0.03), demonstrating increased ATP transfer. PCr/ATP fell (from 2.17 ± 0.2 to 1.99 ± 0.22, p = 0.027). Baseline PCr/ATP positively correlated with the change in stroke volume (R2 = 0.66, p = 0.005) during administration of GTN. In addition, whilst at rest, CK kf correlated with rate pressure product (R2 = 0.56, p = 0.03), there was no correlation seen during GTN.
Conclusions
We have shown vasoplegia increases energy demand upon the heart, despite unchanged cardiac output and rate pressure product. Further, we have shown a fall in Phosphocreatine/ATP ratio, suggesting this ATP transfer outstripped oxidative phosphorylation and the phosphocreatine pool was depleted in order to maintain ATP delivery. We speculate that progressive depletion of energetics in the context of high energy demand drives hearts under constant stress into failure.
In addition, we demonstrate that the magnitude of the resting phosphocreatine pool relates to ability to augment stroke volume during stress and suggest that this may be protective against a decline into failure. Further work is needed, but PCr/ATP may be an important biomarker for treatments that target myocardial energetics to protect against failure. Abstract Figure 1
Prevalence of undiagnosed pre-diabetes or diabetes in patients with HFpEF presenting in the emergency department
Authors: Stratinaki M , Milaki K , Stavrakis S , Pitarokoilis M , Rogdakis E , Charitakis E , Kafarakis P , Garidas G , Stavratis S , Korela D , Katsiavos A , Thanasia A , Lamprogiannakis E , Foukarakis E 
Published: April 2021

Abstract

Funding Acknowledgements
Type of funding sources: None.

Introduction
Heart failure with preserved ejection fraction (HFpEF) has become a common cause of visiting the emergency department (ED). Type 2 diabetes mellitus (T2DM) is one of the important predisposing factors.

Purpose
To study the prevalence of undiagnosed pre-diabetes or T2DM in the patients visiting the ED due to HFpEF.

Methods
93 consecutive patients without known history of T2DM visited the ED with signs and symptoms of heart failure. Left ventricular ejection fraction (LVEF) was calculated using bedside ECHO. LVEF &gt; 50% was used to classify HFpEF patients. HbA1c was measured to all patients and the cutoff for T2DM was HbA1c &gt; 6.5% and for pre-diabetes 5.7-6.4%. Body mass index (BMI), brain natriuretic peptide (BNP) , creatinine and hemoglobin (Hb) were also recorded. Results are interpreted as mean ± SD.

Results
Mean age was 56 ± 11.8 years. 64/93 (68.8%) were female and 29/93(26.97%) male. Mean BMI was 36.52 ± 7.34 kg/m2 and mean Hb 13.51 ± 3.45 g/dl. Mean BNP was 584.82 ± 212.97 pg/ml. Mean creatinine was 1.11 ± 0.36mg/dl. 19/93 (17.67%) patients had HbA1c &gt; 5.7-6.4% and were classified as pre-diabetics and 23/93(21.93%) had HbA1c &gt; 6.5% and were classified as diabetics. We did not identify any correlation between the rest of the parameters.

Coclusion
44.64% of the patients that visited ED due to signs or symptoms of HFpEF were identified as having either pre-diabetes or T2DM. Taking into consideration the importance of the presence of T2DM in the prognosis of the patients with HFpEF, it would be reasonable to screen all patients with HFpEF for T2DM and suggest specialized treatment.
Bleeding predictors in acute coronary syndrome: does the age or clinical presentation matters?
Authors: Marques Pires C , Campos I , Medeiros P , Flores R , Mane F , Azevedo P , Galvao Braga C , Pereira MA , Gaspar A 
Published: April 2021

Abstract

Funding Acknowledgements
Type of funding sources: None.

INTRODUCTION
Bleeding is a quite common non-cardiac complication of acute coronary syndrome (ACS) and is associated with a negative prognosis impact.

AIMS
To determine the predictors of inhospital major bleeding (IHMB) in ACS and to evaluate whether they differ according to age and clinical presentation.

METHODS
A multicentric retrospective study which analysed 25524 patients(pts) with ACS, 25141 without and 383 with IHMB.
By multivariate analysis, we determined IHMB predictors and evaluated the differences between age groups (&lt;80 years; ≥80 years) and clinical presentation- ST elevation myocardial infarction (STEMI) or non-ST elevation ACS (NSTEACS).

RESULTS
By multivariate analysis we found 15 significant IHMB predictors (pvalue &lt; 0,05): age≥75years, hypertension, previous angina, pulmonary disease, previous bleeding, atypical presentation (without pain), cardiac arrest, admission heart rate (HR)&gt;100bpm, Killip4 at admission, ST-elevation, admission haemoglobin (Hb)&lt;10g/dL, aspirin or Vitamin K antagonist (VKA) or ivabradine as previous medication and glycoprotein IIb/IIIa inhibitors (GPIIb/IIIa) use.
Then, we made a sub-analysis in STEMI pts which revealed that IHMB predictors of pts &lt;80 years were: female gender, age≥75years, chronic kidney disease (CKD), active neoplasm, previous bleeding, atypical presentation, cardiac arrest, admission HR &gt; 100bpm, Killip IV on admission and GPIIb/IIIa use. By contrast, IHMB predictors of pts with ≥80 years were: valvular disease, atypical presentation, aspirin as previous medication and GPIIb/IIIa use.
Finally, we made a sub-analysis in NSTACS pts which revealed that IHMB predictors of pts &lt;80years were: previous angina, CKD, previous bleeding, cardiac arrest, Killip≥2 at admission, admission Hb &lt; 10g/dL and VKA as previous medication. Conversely, IHMB predictors of pts with ≥80 years were previous bleeding, cardiac arrest and absence of normal QRS.
In addition, by multivariate analysis we found that IHMB had an impact on inhospital mortality (OR = 2,2;pvalue &lt; 0,001), however, by Cox regression there wasn’t an impact on 1-year mortality.

CONCLUSION
This study suggests that IHMB has impact on inhospital mortality and that its predictors differ with age and clinical presentation. The most powerful predictor was previous bleeding. Considering the importance of IHMB, increased efforts are needed to tailor antithrombotic therapy according to age, renal function and other comorbidities.