bluuebunny/crossref_metadata_2025_split huggingface dataset:
A random-walk-based epidemiological model
Authors: Chu Andrew , Huber Greg , McGeever Aaron , Veytsman Boris , Yllanes David 
Published: September 2021

AbstractRandom walkers on a two-dimensional square lattice are used to explore the spatio-temporal growth of an epidemic. We have found that a simple random-walk system generates non-trivial dynamics compared with traditional well-mixed models. Phase diagrams characterizing the long-term behaviors of the epidemics are calculated numerically. The functional dependence of the basic reproductive number $$R_{0}$$

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0

on the model’s defining parameters reveals the role of spatial fluctuations and leads to a novel expression for $$R_{0}$$

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0

. Special attention is given to simulations of inter-regional transmission of the contagion. The scaling of the epidemic with respect to space and time scales is studied in detail in the critical region, which is shown to be compatible with the directed-percolation universality class.
Controlling for human population stratification in rare variant association studies
Authors: Bouaziz Matthieu , Mullaert Jimmy , Bigio Benedetta , Seeleuthner Yoann , Casanova Jean-Laurent , Alcais Alexandre , Abel Laurent , Cobat Aurélie 
Published: September 2021

AbstractPopulation stratification is a confounder of genetic association studies. In analyses of rare variants, corrections based on principal components (PCs) and linear mixed models (LMMs) yield conflicting conclusions. Studies evaluating these approaches generally focused on limited types of structure and large sample sizes. We investigated the properties of several correction methods through a large simulation study using real exome data, and several within- and between-continent stratification scenarios. We considered different sample sizes, with situations including as few as 50 cases, to account for the analysis of rare disorders. Large samples showed that accounting for stratification was more difficult with a continental than with a worldwide structure. When considering a sample of 50 cases, an inflation of type-I-errors was observed with PCs for small numbers of controls (≤ 100), and with LMMs for large numbers of controls (≥ 1000). We also tested a novel local permutation method (LocPerm), which maintained a correct type-I-error in all situations. Powers were equivalent for all approaches pointing out that the key issue is to properly control type-I-errors. Finally, we found that power of analyses including small numbers of cases can be increased, by adding a large panel of external controls, provided an appropriate stratification correction was used.
Moringa oleifera seeds-removed ripened pods as alternative for papersheet production: antimicrobial activity and their phytoconstituents profile using HPLC
Authors: Salem Mohamed Z. M. , Ali Hayssam M. , Akrami Mohammad 
Published: September 2021

AbstractIn the present study, and for the waste valorization,Moringa oleiferaseeds-removed ripened pods (SRRP) were used for papersheet production and for the extraction of bioactive compounds. Fibers were characterized by SEM–EDX patterns, while the phytoconstituents in ethanol extract was analyzed by HPLC. The inhibition percentage of fungal mycelial growth (IFMG) of the treatedMelia azedarachwood withM. oleiferaSRRP extract at the concentrations of 10,000, 20,000, and 30,000 µg/mL against the growth ofRhizoctonia solaniandFusarium culmorumwas calculated and compared with fluconazole (25 µg). The produced papersheet was treated with the ethanol extract (4000, 2000, and 1000 µg/mL) and assayed for its antibacterial activity againstAgrobacterium tumefaciens,Erwinia amylovora, andPectobacterium atrosepticumby measuring the inhibition zones and minimum inhibitory concentrations (MICs). According to chemical analysis ofM. oleiferaSRRP, benzene:alcohol extractives, holocellulose, lignin, and ash contents were 7.56, 64.94, 25.66 and 1.53%, respectively, while for the produced unbleached pulp, the screen pulp yield and the Kappa number were 39% and 25, respectively. The produced papersheet showed tensile index, tear index, burst index, and double fold number values of 58.8 N m/g, 3.38 mN m2/g, 3.86 kPa m2/g, and 10.66, respectively. SEM examination showed that the average fiber diameter was 16.39 µm, and the mass average of for elemental composition of C and O by EDX were, 44.21%, and 55.79%, respectively. The main phytoconstituents in the extract (mg/100 g extract) by HPLC were vanillic acid (5053.49), benzoic acid (262.98), naringenin (133.02), chlorogenic acid (66.16), and myricetin (56.27). After 14 days of incubation,M. oleiferaSRRP extract-wood treated showed good IFMG againstR. solani(36.88%) andF. culmorum(51.66%) compared to fluconazole, where it observed 42.96% and 53.70%, respectively. Moderate to significant antibacterial activity was found, where the minimum inhibitory concentration (MIC) values were 500, 650, and 250 µg/mL against the growth ofA. tumefaciens,E. amylovora, andP. atrosepticumrespectively, which were lower than the positive control used (Tobramycin 10 µg/disc). In conclusion,M. oleiferaSRRP showed promising properties as a raw material for pulp and paper production as well as for the extraction of bioactive compounds.
Visual explanations from spiking neural networks using inter-spike intervals
Authors: Kim Youngeun , Panda Priyadarshini 
Published: September 2021

AbstractBy emulating biological features in brain, Spiking Neural Networks (SNNs) offer an energy-efficient alternative to conventional deep learning. To make SNNs ubiquitous, a ‘visual explanation’ technique for analysing and explaining the internal spike behavior of such temporal deep SNNs is crucial. Explaining SNNs visually will make the network more transparent giving the end-user a tool to understand how SNNs make temporal predictions and why they make a certain decision. In this paper, we propose a bio-plausible visual explanation tool for SNNs, called Spike Activation Map (SAM). SAM yields a heatmap (i.e., localization map) corresponding to each time-step of input data by highlighting neurons with short inter-spike interval activity. Interestingly, without the use of gradients and ground truth, SAM produces a temporal localization map highlighting the region of interest in an image attributed to an SNN’s prediction at each time-step. Overall, SAM outsets the beginning of a new research area ‘explainable neuromorphic computing’ that will ultimately allow end-users to establish appropriate trust in predictions from SNNs.
Isolation and characterization of a lytic bacteriophage against Pseudomonas aeruginosa
Authors: Sharma Sonika , Datta Sibnarayan , Chatterjee Soumya , Dutta Moumita , Samanta Jhuma , Vairale Mohan G. , Gupta Rajeev , Veer Vijay , Dwivedi Sanjai K. 
Published: September 2021

AbstractIn recent years, the use of bacteriophages (or 'phages') against multidrug-resistant (MDR) bacteria including Pseudomonas aeruginosa has drawn considerable attention, globally. In this work, we report the isolation and detailed characterization of a highly lytic Pseudomonasphage DRL-P1 isolated from wastewater. Under TEM, DRL-P1 appeared as a member of the phage family Myoviridae. DRL-P1 featured rapid adsorption (~ 5 min), short-latency (~ 30 min), and large burst size (~ 100 PFU per infected cell). DRL-P1 can withstand a wide temperature range (4 °C to 40 °C) and pH (5.0 to 10.0) conditions. The 66,243 bp DRL-P1 genome (MN564818) encodes at least 93 ORFs, of which 36 were functionally annotated based on homology with similar phage proteins available in the databases. Comparative analyses of related genomes suggest an independent evolutionary history and discrete taxonomic position of DRL-P1 within genus Pbunavirus. No toxin or antibiotic resistance genes was identified. DRL-P1 is tolerant to lyophilization and encapsulation techniques and retained lytic activity even after 18 months of storage. We also demonstrated decontaminating potentials of DRL-P1 in vitro, on an artificially contaminated cover-slip model. To the best of our knowledge, this is the first Pbunavirus to be reported from India. Our study suggests DRL-P1 as a potential candidate for various applications.
Prevalence of elevated serum fatty acid synthase in chronic limb-threatening ischemia
Authors: Tay Shirli , De Silva Gayan S. , Engel Connor M. , Harroun Nikolai , Penrose Amanda S. , Desai Kshitij A. , Yan Yan , Semenkovich Clay F. , Zayed Mohamed A. 
Published: September 2021

AbstractThere are currently no serum-based evaluations that can corroborate the severity of peripheral artery disease (PAD). In this cross-sectional study, we assessed the prevalence of elevated serum fatty acid synthase (cFAS) in patients with chronic limb-threatening ischemia (CLTI) and evaluated the accuracy of its use in detecting this condition. Preoperative fasting serum samples from 87 patients undergoing vascular intervention were collected between October 2014 and September 2016. Median age was 62 years, with 56 (64%) men, and 32 (37%) with CLTI. We found that elevated cFAS content (OR 1.17; 95% CI 1.04–1.31), type 2 diabetes (T2D; OR 5.22; 95% CI 1.77–15.4), and smoking (OR 3.53; 95% CI 1.19–10.5) were independently associated with CLTI and could detect the presence of CLTI with 83% accuracy (95% CI 0.74–0.92). Furthermore, serum FAS content was positively correlated with FAS content in femoral artery plaque in patients with severe PAD ($${R}^{2}$$

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2

= 0.22; P =  0.023). Finally, significantly higher co-localization of FAS and ApoB were observed within lower extremity arterial media (P < .001). Our findings indicate that serum FAS content is a marker for disease severity in patients with PAD, independent of concomitant T2D and smoking, and may play a key role in FAS and ApoB peripheral plaque progression.
Prospective postmortem evaluation of 735 consecutive SARS-CoV-2-associated death cases
Authors: Fitzek Antonia , Schädler Julia , Dietz Eric , Ron Alexandra , Gerling Moritz , Kammal Anna L. , Lohner Larissa , Falck Carla , Möbius Dustin , Goebels Hanna , Gerberding Anna-Lina , Schröder Ann Sophie , Sperhake Jan-Peter , Klein Anke , Fröb Daniela , Mushumba Herbert , Wilmes Sandra , Anders Sven , Kniep Inga , Heinrich Fabian , Langenwalder Felicia , Meißner Kira , Lange Philine , Zapf Antonia , Püschel Klaus , Heinemann Axel , Glatzel Markus , Matschke Jakob , Aepfelbacher Martin , Lütgehetmann Marc , Steurer Stefan , Thorns Christoph , Edler Carolin , Ondruschka Benjamin 
Published: September 2021

AbstractCoronavirus disease 19 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a global pandemic with significant mortality. Accurate information on the specific circumstances of death and whether patients died from or with SARS-CoV-2 is scarce. To distinguish COVID-19 from non-COVID-19 deaths, we performed a systematic review of 735 SARS-CoV-2-associated deaths in Hamburg, Germany, from March to December 2020, using conventional autopsy, ultrasound-guided minimally invasive autopsy, postmortem computed tomography and medical records. Statistical analyses including multiple logistic regression were used to compare both cohorts. 84.1% (n = 618) were classified as COVID-19 deaths, 6.4% (n = 47) as non-COVID-19 deaths, 9.5% (n = 70) remained unclear. Median age of COVID-19 deaths was 83.0 years, 54.4% were male. In the autopsy group (n = 283), the majority died of pneumonia and/or diffuse alveolar damage (73.6%; n = 187). Thromboses were found in 39.2% (n = 62/158 cases), pulmonary embolism in 22.1% (n = 56/253 cases). In 2020, annual mortality in Hamburg was about 5.5% higher than in the previous 20 years, of which 3.4% (n = 618) represented COVID-19 deaths. Our study highlights the need for mortality surveillance and postmortem examinations. The vast majority of individuals who died directly from SARS-CoV-2 infection were of advanced age and had multiple comorbidities.
Serum carcinoembryonic antigen elevation in benign lung diseases
Authors: Yang Yi , Xu Mingfang , Huang Huan , Jiang Xiaolin , Gong Kan , Liu Yun , Kuang Xunjie , Yang Xueqin 
Published: September 2021

AbstractCarcinoembryonic antigen (CEA) is not only used to aid the diagnosis of lung cancer, but also help monitor recurrence and determine the prognosis of lung cancer as well as evaluate the therapeutic efficacy for lung cancer. However, studies have also shown that CEA is present at low levels in the serum of patients with benign lung diseases (BLD), which will interfere with the accurate judgment of the disease. Due to difference in sample size, detection methods, cutoff values and sources of BLD, the positive rate of CEA in BLD is different with different literature. Therefore, it is necessary to define CEA levels in patients of different BLD in a large sample study. 4796 patients with BLD were included in this study. The results showed that the CEA levels of 3.1% (149/4796) patients with BLD were elevated, with three cases exceeds 20 ng/mL (0.06%, 3/4796). The results from the literature showed that BLD had a mean positive rate of 5.99% (53/885) and only two cases had CEA above 20 ng/mL. The CEA elevations mainly distributed in chronic obstructive pulmonary disease (COPD), pneumonitis and interstitial lung disease and significantly correlated with age of patients (OR 2.69, 95% CI 1.94–3.73, p < 0.001). Pulmonary tuberculosis (7/1311, 0.53%) had the lowest positive rate of CEA elevations while pulmonary alveolar proteinosis (6/27, 22.22%) had the highest positive rate. The majority of patients with abnormally elevated CEA levels had multiple underlying diseases, mainly diseases of the circulatory system (42.28% [63/149]), endocrine diseases (26.85% [40/149]), and respiratory or heart failure (24.16% [36/149]. In endocrine diseases, 87.5% (35/40) of patients had diabetes. In conclusion, CEA is present at a low positive rate in the serum of patients with BLD, but few exceed 20 ng/mL. For lung disease patients, if CEA levels rise, we should carry out comprehensive analysis of types of lung diseases, age of patients, and comorbid diseases.
Broad scale proteomic analysis of heat-destabilised symbiosis in the hard coral Acropora millepora
Authors: Petrou K. , Nunn B. L. , Padula M. P. , Miller D. J. , Nielsen D. A. 
Published: September 2021

AbstractCoral reefs across the globe are threatened by warming oceans. The last few years have seen the worst mass coral bleaching events recorded, with more than one quarter of all reefs irreversibly impacted. Considering the widespread devastation, we need to increase our efforts to understanding the physiological and metabolic shifts underlying the breakdown of this important symbiotic ecosystem. Here, we investigated the proteome (PRIDE accession # PXD011668) of both host and symbionts of the reef-building coralAcropora milleporaexposed to ambient (~ 28 °C) and elevated temperature (~ 32 °C for 2 days, following a five-day incremental increase) and explored associated biomolecular changes in the symbiont, with the aim of gaining new insights into the mechanisms underpinning the collapse of the coral symbiosis. We identified 1,230 unique proteins (774 host and 456 symbiont) in the control and thermally stressed corals, of which 107 significantly increased and 125 decreased in abundance under elevated temperature relative to the control. Proteins involved in oxidative stress and proteolysis constituted 29% of the host proteins that increased in abundance, with evidence of impairment to endoplasmic reticulum and cytoskeletal regulation proteins. In the symbiont, we detected a decrease in proteins responsible for photosynthesis and energy production (33% of proteins decreased in abundance), yet minimal signs of oxidative stress or proteolysis. Lipid stores increased > twofold despite reduction in photosynthesis, suggesting reduced translocation of carbon to the host. There were significant changes in proteins related to symbiotic state, including proteins linked to nitrogen metabolism in the host and the V-ATPase (-0.6 fold change) known to control symbiosome acidity. These results highlight key differences in host and symbiont proteomic adjustments under elevated temperature and identify two key proteins directly involved in bilateral nutrient exchange as potential indicators of symbiosis breakdown.
Mutual inhibition effect of sulfur compounds in the hydrodesulfurization of thiophene, 2-ethylthiophene and benzothiophene ternary mixture
Authors: Calin Catalina , Leostean Cristian , Trifoi Ancuța Roxana , Oprescu Elena-Emilia , Wiita Elizabeth , Banu Ionut , Doukeh Rami 
Published: September 2021

AbstractThe hydrodesulphurization of a model component and equimolar ternary mixture of thiophene, 2-ethylthiophene and benzothiophene over sulphided CoMo/γ-Al2O3 and CoMo/γ-Al2O3-Nb2O5 catalysts were investigated in a fixed bed flow reactor. The catalysts were prepared by incipient wetness impregnation method and characterized by textural characteristics, total acidity and chemical species present on the catalysts surface. The characterization results showed that both CoMo/γ-Al2O3-Nb2O5 and sulphided CoMo/γ-Al2O3 catalysts exhibit a mesoporous structure with cylindrical pores open at both ends, evidenced by the IV type adsorption–desorption isotherm with a H1 hysteresis loop and have an average pore diameter between 3 and 4 nm. The chemical species present on the catalysts surface evaluated by XPS indicated that Co2+ and Mo4+ species are present in the sulfide form on both catalysts surfaces. In addition, there are also found oxidic species arising from incomplete reduction and sulphidation. The presence of niobium oxide in the catalytic support had a positive effect in leading to higher specific surface area (170 m2/g) and total acidity (0.421 meq/g) compared with CoMo/γ-Al2O3 catalyst (140 m2/g and 0.283 meq/g) respectively. The evaluation results from the hydrodesulfurization showed that CoMo/γ-Al2O3-Nb2O5 catalyst had a higher activity in hydrodesulphurization process of thiophene, 2-ethylthiophene and benzothiophene. The CoMo/γ-Al2O3-Nb2O5 catalyst eliminated sulfur from the single component feed (corresponding to 2380 ppm S) and reduced below 10 ppm, for the feed consisting in the equimolar ternary mixture of thiophene, 2-ethylthiophene and benzothiophene (2380 ppm S). The reactivity of thiophen compounds was reduced due to competitive adsorption. It was observed that benzothiophene inhibits the transformation of thiophene and 2-ethylthiophene. A mutual inhibition effect between sulfur compounds was also observed when thiophene, 2-ethylthiophene and benzothiophene were combined and tested over the CoMo/γ-Al2O3 catalyst. The inhibition effect had a lower intensity by introducing Nb2O5 in the catalyst support.
Optimizing thermocouple’s ZT through design innovation
Authors: Zhang Tinggang 
Published: September 2021

AbstractThis work demonstrates that in parallel with the one existed at high doping concentration, there also exists an optimal combination of the transport properties of a thermoelectric material at low doping concentration as the curve of the relation between electrical conductivity and doping concentration is rigidly shifted toward that direction without disturbing the Seebeck coefficient and the thermal conductivity. Based on this finding, a new thermocouple design that uses low doping legs and high doping semiconductors as the external carrier injectors surrounding the legs is developed. The analytical model developed for the new thermocouple indicated that its efficiency and power output could be more than tripled as compared to those of the original design. A single thermocouple made of Silicon semiconductors was simulated numerically using different sets of input parameters. The results showed that the density of the externally injected carriers played a significant role in enhancing the thermocouple’s efficiency and power output.
Altered microRNA and mRNA profiles during heart failure in the human sinoatrial node
Authors: Li Ning , Artiga Esthela , Kalyanasundaram Anuradha , Hansen Brian J. , Webb Amy , Pietrzak Maciej , Biesiadecki Brandon , Whitson Bryan , Mokadam Nahush A. , Janssen Paul M. L. , Hummel John D. , Mohler Peter J. , Dobrzynski Halina , Fedorov Vadim V. 
Published: September 2021

AbstractHeart failure (HF) is frequently accompanied with the sinoatrial node (SAN) dysfunction, which causes tachy-brady arrhythmias and increased mortality. MicroRNA (miR) alterations are associated with HF progression. However, the transcriptome of HF human SAN, and its role in HF-associated remodeling of ion channels, transporters, and receptors responsible for SAN automaticity and conduction impairments is unknown. We conducted comprehensive high-throughput transcriptomic analysis of pure human SAN primary pacemaker tissue and neighboring right atrial tissue from human transplanted HF hearts (n = 10) and non-failing (nHF) donor hearts (n = 9), using next-generation sequencing. Overall, 47 miRs and 832 mRNAs related to multiple signaling pathways, including cardiac diseases, tachy-brady arrhythmias and fibrosis, were significantly altered in HF SAN. Of the altered miRs, 27 are predicted to regulate mRNAs of major ion channels and neurotransmitter receptors which are involved in SAN automaticity (e.g. HCN1, HCN4, SLC8A1) and intranodal conduction (e.g. SCN5A, SCN8A) or both (e.g. KCNJ3, KCNJ5). Luciferase reporter assays were used to validate interactions of miRs with predicted mRNA targets. In conclusion, our study provides a profile of altered miRs in HF human SAN, and a novel transcriptome blueprint to identify molecular targets for SAN dysfunction and arrhythmia treatments in HF.
Efficacy and tolerability of the hexanic extract of Serenoa repens compared to tamsulosin in moderate-severe LUTS-BPH patients
Authors: Alcaraz Antonio , Rodríguez-Antolín Alfredo , Carballido-Rodríguez Joaquín , Castro-Díaz David , Medina-Polo José , Fernández-Gómez Jesús M. , Ficarra Vincenzo , Palou Joan , Ponce de León Roca Javier , Angulo Javier C. , Esteban-Fuertes Manuel , Cózar-Olmo José M. , Pérez-León Noemí , Molero-García José M. , Fernández-Pro Ledesma Antonio , Brenes-Bermúdez Francisco J. , Manasanch José 
Published: September 2021

AbstractIn a subset analysis of data from a 6-month, multicenter, non-interventional study, we compared change in symptoms and quality of life (QoL), and treatment tolerability, in men with moderate to severe lower urinary tract symptoms associated with benign prostatic hyperplasia (LUTS/BPH) receiving tamsulosin (TAM, 0.4 mg/day) or the hexanic extract of Serenoa repens (HESr, 320 mg/day) as monotherapy. Symptoms and QoL were assessed using the IPSS and BII questionnaires, respectively. Patients in the treatment groups were matched using two statistical approaches (iterative and propensity score matching). Within the iterative matching approach, data was available from a total of 737 patients (353 TAM, 384 HESr). After 6 months, IPSS scores improved by a mean (SD) of 5.0 (4.3) points in the TAM group and 4.5 (4.7) points in the HESr group (p = 0.117, not significant). Improvements in QoL were equivalent in the two groups. TAM patients reported significantly more adverse effects than HESr patients (14.7% vs 2.1%; p < 0.001), particularly ejaculation dysfunction and orthostatic hypotension. These results show that HESr is a valid treatment option for men with moderate/severe LUTS/BPH; improvements in urinary symptoms and QoL were similar to those observed for tamsulosin, but with considerably fewer adverse effects.