bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low cost electrical probe station using etched tungsten nanoprobes: role of cathode geometry
Authors: Prasad Rakesh K , Singh Dilip K 
Published: September 2020

Abstract
Electrical measurement of nano-scale devices and structures requires skills and hardware to make nano-contacts. Such measurements have been difficult for number of laboratories due to cost of probe station and nano-probes. In the present work, we have demonstrated possibility of assembling low cost probe station using USB microscope (US $ 30) coupled with in-house developed probe station. We have explored the effect of shape of etching electrodes on the geometry of the microprobes developed. The variation in the geometry of copper wire electrode is observed to affect the probe length

(
0.58

mm

to

2.15

mm
)

and its half cone angle (1.4° to 8.8˚). These developed probes were used to make contact on micro patterned metal films and was used for electrical measurement along with semiconductor parameter analyzer. These probes show low contact resistance (∼4 Ω) and follows ohmic behavior. Such probes can be used for laboratories involved in teaching and multidisciplinary research activities and Atomic Force Microscopy.
Feasible-metabolic-pathway-exploration technique using chemical latent space
Authors: Fuji Taiki , Nakazawa Shiori , Ito Kiyoto 
Published: September 2020

Abstract

Motivation
Exploring metabolic pathways is one of the key techniques for developing highly productive microbes for the bioproduction of chemical compounds. To explore feasible pathways, not only examining a combination of well-known enzymatic reactions but also finding potential enzymatic reactions that can catalyze the desired structural changes are necessary. To achieve this, most conventional techniques use manually predefined-reaction rules, however, they cannot sufficiently find potential reactions because the conventional rules cannot comprehensively express structural changes before and after enzymatic reactions. Evaluating the feasibility of the explored pathways is another challenge because there is no way to validate the reaction possibility of unknown enzymatic reactions by these rules. Therefore, a technique for comprehensively capturing the structural changes in enzymatic reactions and a technique for evaluating the pathway feasibility are still necessary to explore feasible metabolic pathways.

Results
We developed a feasible-pathway-exploration technique using chemical latent space obtained from a deep generative model for compound structures. With this technique, an enzymatic reaction is regarded as a difference vector between the main substrate and the main product in chemical latent space acquired from the generative model. Features of the enzymatic reaction are embedded into the fixed-dimensional vector, and it is possible to express structural changes of enzymatic reactions comprehensively. The technique also involves differential-evolution-based reaction selection to design feasible candidate pathways and pathway scoring using neural-network-based reaction-possibility prediction. The proposed technique was applied to the non-registered pathways relevant to the production of 2-butanone, and successfully explored feasible pathways that include such reactions.
synergy: a Python library for calculating, analyzing and visualizing drug combination synergy
Authors: Wooten David J , Albert Réka 
Published: September 2020

Abstract

Summary
Combinations of multiple pharmacological agents can achieve a substantial benefit over treatment with single agents alone. Combinations that achieve ‘more than the sum of their parts’ are called synergistic. There have been many proposed frameworks to understand and quantify drug combination synergy with different assumptions and domains of applicability. We introduce here synergy, a Python library that (i) implements a broad array of popular synergy models, (ii) provides tools for evaluating confidence intervals and conducting power analysis and (iii) provides standardized tools to analyze and visualize drug combinations and their synergies and antagonisms.

Availability and implementation
synergy is available on all operating systems for Python &gt;=3.5. It is freely available from https://pypi.org/project/synergy, and its source code is available at https://github.com/djwooten/synergy. This software is released under the GNU General Public License, version 3.0 or later.

Supplementary information
Supplementary data are available at Bioinformatics online.
Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data
Authors: Schreiber Jacob , Bilmes Jeffrey , Noble William Stafford 
Published: September 2020

Abstract

Motivation
Successful science often involves not only performing experiments well, but also choosing well among many possible experiments. In a hypothesis generation setting, choosing an experiment well means choosing an experiment whose results are interesting or novel. In this work, we formalize this selection procedure in the context of genomics and epigenomics data generation. Specifically, we consider the task faced by a scientific consortium such as the National Institutes of Health ENCODE Consortium, whose goal is to characterize all of the functional elements in the human genome. Given a list of possible cell types or tissue types (‘biosamples’) and a list of possible high-throughput sequencing assays, where at least one experiment has been performed in each biosample and for each assay, we ask ‘Which experiments should ENCODE perform next?’

Results
We demonstrate how to represent this task as a submodular optimization problem, where the goal is to choose a panel of experiments that maximize the facility location function. A key aspect of our approach is that we use imputed data, rather than experimental data, to directly answer the posed question. We find that, across several evaluations, our method chooses a panel of experiments that span a diversity of biochemical activity. Finally, we propose two modifications of the facility location function, including a novel submodular–supermodular function, that allow incorporation of domain knowledge or constraints into the optimization procedure.

Availability and implementation
Our method is available as a Python package at https://github.com/jmschrei/kiwano and can be installed using the command pip install kiwano. The source code used here and the similarity matrix can be found at http://doi.org/10.5281/zenodo.3708538.

Supplementary information
Supplementary data are available at Bioinformatics online.
Acetylcholine ameliorated TNF-α-induced primary trophoblast malfunction via muscarinic receptors†
Authors: Wang Zheng , Zibrila Adoulaye Issotina , Liu Shuhua , Zhao Gongxiao , Li Yubei , Xu Jingning , Liu Dan , Li Chunfang , Feng Weiyi , Liu Jinjun 
Published: September 2020

Abstract
Oxidative stress and apoptosis of trophoblasts are involved in preeclampsia (PE). Numerous studies have shown that acetylcholine (ACh), the principal vagal neurotransmitter, plays a crucial role in attenuating oxidative stress, inflammation, and apoptosis in a variety of human diseases. However, the role of ACh in PE management remains unclear. Here, we aimed to determine the effects of ACh on TNF-α-treated human primary trophoblast cells. Western blotting, CCK-8, DHE, TUNEL immunofluorescence staining, transwell assays, and wound-healing assays were performed to evaluate the role of ACh in vitro. We found that both TNF-α expression and the apoptotic index were higher in placentas from preeclamptic women than in normal placentas. TNF-α enhanced oxidative stress and increased the number of TUNEL-positive nuclei, Bax/Bcl-2 ratio, and the cleaved caspase-3/caspase-3 ratio while decreasing cell viability in primary human trophoblast cells. TNF-α promoted cell migration and invasion. PDTC, a selective NF-κB inhibitor, significantly blunted TNF-α-induced effects. ACh treatment attenuated oxidative stress and apoptosis while further promoting migration and invasion of TNF-α-treated primary trophoblast cells. The effects of ACh could be reversed by the muscarinic receptor antagonist atropine. Overall, our findings indicate that ACh significantly ameliorates TNF-α-induced oxidative stress and apoptosis of human primary trophoblast cells via muscarinic receptors. This is the first time that the improvement of vagal activity served as a therapeutic strategy for PE-like trophoblasts, suggesting its potential value in clinical practice.
Lack of effect of short-term DHEA supplementation on the perimenopausal ovary†
Authors: Luna Selva L , Brown Donald I , Kohama Steven G , Urbanski Henryk F 
Published: September 2020

Abstract
Dehydroepiandrosterone (DHEA) hormonal supplementation can improve oocyte quality in women with diminished ovarian function. However, it is unclear whether DHEA supplementation can also enhance ovarian function during the perimenopause (i.e., when the number of follicles in the ovary has undergone a marked reduction). To address this question, we examined the impact of 2.5-months of daily 5-mg oral DHEA supplementation on the number of ovarian follicles and the concentration of anti-Müllerian hormone (AMH) in perimenopausal rhesus macaques. Like women, these long-lived nonhuman primates have ~ 28-day menstrual cycles and eventually undergo menopause. They also show similar age-related neuroendocrine changes, including a marked decrease in circulating concentrations of DHEA and DHEA sulfate (DHEAS). Our experimental design involved the following three groups of animals (N = 6 per group): Young adult (mean age = 11.6 years), Old control (mean age = 23.1 years), and Old DHEA-treated (mean age = 23.5 years). Histological examination of the ovaries revealed a significant age-related decrease in the mean number of primordial follicles despite DHEA supplementation. Moreover, AMH concentrations within the ovaries and circulation, assessed by Western analysis and ELISA, respectively, showed significant age-related decreases that were not attenuated by DHEA supplementation. Taken together, these results fail to show a clear effect of short-term physiological DHEA supplementation on the perimenopausal ovary. However, they do not exclude the possibility that alternative DHEA supplementation paradigms (e.g., involving an earlier start date, longer duration and using pharmacological doses) may extend reproductive potential during aging.
Pathophysiological subtypes of Alzheimer’s disease based on cerebrospinal fluid proteomics
Authors: Tijms Betty M , Gobom Johan , Reus Lianne , Jansen Iris , Hong Shengjun , Dobricic Valerija , Kilpert Fabian , ten Kate Mara , Barkhof Frederik , Tsolaki Magda , Verhey Frans R J , Popp Julius , Martinez-Lage Pablo , Vandenberghe Rik , Lleó Alberto , Molinuevo José Luís , Engelborghs Sebastiaan , Bertram Lars , Lovestone Simon , Streffer Johannes , Vos Stephanie , Bos Isabelle ,   The Alzheimer’s Disease Neuroimaging Initiative (ADNI), Blennow Kaj , Scheltens Philip , Teunissen Charlotte E , Zetterberg Henrik , Visser Pieter Jelle 
Published: September 2020

Abstract
Alzheimer’s disease is biologically heterogeneous, and detailed understanding of the processes involved in patients is critical for development of treatments. CSF contains hundreds of proteins, with concentrations reflecting ongoing (patho)physiological processes. This provides the opportunity to study many biological processes at the same time in patients. We studied whether Alzheimer’s disease biological subtypes can be detected in CSF proteomics using the dual clustering technique non-negative matrix factorization. In two independent cohorts (EMIF-AD MBD and ADNI) we found that 705 (77% of 911 tested) proteins differed between Alzheimer’s disease (defined as having abnormal amyloid, n = 425) and controls (defined as having normal CSF amyloid and tau and normal cognition, n = 127). Using these proteins for data-driven clustering, we identified three robust pathophysiological Alzheimer’s disease subtypes within each cohort showing (i) hyperplasticity and increased BACE1 levels; (ii) innate immune activation; and (iii) blood–brain barrier dysfunction with low BACE1 levels. In both cohorts, the majority of individuals were labelled as having subtype 1 (80, 36% in EMIF-AD MBD; 117, 59% in ADNI), 71 (32%) in EMIF-AD MBD and 41 (21%) in ADNI were labelled as subtype 2, and 72 (32%) in EMIF-AD MBD and 39 (20%) individuals in ADNI were labelled as subtype 3. Genetic analyses showed that all subtypes had an excess of genetic risk for Alzheimer’s disease (all P &gt; 0.01). Additional pathological comparisons that were available for a subset in ADNI suggested that subtypes showed similar severity of Alzheimer’s disease pathology, and did not differ in the frequencies of co-pathologies, providing further support that found subtypes truly reflect Alzheimer’s disease heterogeneity. Compared to controls, all non-demented Alzheimer’s disease individuals had increased risk of showing clinical progression (all P &lt; 0.01). Compared to subtype 1, subtype 2 showed faster clinical progression after correcting for age, sex, level of education and tau levels (hazard ratio = 2.5; 95% confidence interval = 1.2, 5.1; P = 0.01), and subtype 3 at trend level (hazard ratio = 2.1; 95% confidence interval = 1.0, 4.4; P = 0.06). Together, these results demonstrate the value of CSF proteomics in studying the biological heterogeneity in Alzheimer’s disease patients, and suggest that subtypes may require tailored therapy.
Surveying Chemosensory Dysfunction in COVID-19
Authors: Green Barry G 
Published: September 2020

Abstract
Soon after the outbreak of COVID-19, reports that smell and taste are disrupted by the illness drew the attention of chemosensory scientists and clinicians throughout the world. While other upper respiratory viruses are known to produce such disruptions, their occurrence with the deadly and highly infectious SARS-CoV-2 virus raised new questions about the nature of the deficits, their cause, and whether they might serve as indicators of the onset of the disease. Published in the July and August 2020 issues of Chemical Senses are 2 innovative, large-scale survey studies that were quickly devised and launched by separate multinational groups to address these questions in olfaction, taste, and chemesthesis. The surveys, which took different approaches and had somewhat different goals, add significant new data on the incidence and severity of smell loss in COVID-19, and the potential for olfactory dysfunction to serve as an indicator of the spread and severity of the disease. Less definitive evidence of the frequency, characteristics, and magnitude of disruptions in taste and chemesthesis point to the need for future survey studies that combine and refine the strengths of the present ones, as well as clinical studies designed to selectively measure deficits in all 3 chemosensory systems.
Central Nervous System Safety During Brief Analytic Treatment Interruption of Antiretroviral Therapy Within 4 Human Immunodeficiency Virus Remission Trials: An Observational Study in Acutely Treated People Living With Human Immunodeficiency Virus
Authors: Hellmuth Joanna , Muccini Camilla , Colby Donn J , Kroon Eugène , de Souza Mark , Crowell Trevor A , Chan Phillip , Sacdalan Carlo , Intasan Jintana , Benjapornpong Khunthalee , Tipsuk Somporn , Puttamaswin Suwanna , Chomchey Nitiya , Valcour Victor , Sarnecki Michal , Tomaka Frank , Krebs Shelly J , Slike Bonnie M , Jagodzinski Linda L , Dumrongpisutikul Netsiri , Sailasuta Napapon , Samboju Vishal , Michael Nelson L , Robb Merlin L , Vasan Sandhya , Ananworanich Jintanat , Phanuphak Praphan , Phanuphak Nittaya , Paul Robert , Spudich Serena 
Published: September 2020

AbstractBackgroundThe central nervous system (CNS) is a likely reservoir of human immunodeficiency virus (HIV), vulnerable to viral rebound, inflammation, and clinical changes upon stopping antiretroviral therapy (ART). It is critical to evaluate the CNS safety of studies using analytic treatment interruption (ATI) to assess HIV remission.MethodsThirty participants who started ART during acute HIV infection underwent CNS assessments across 4 ATI remission trials. ART resumption occurred with plasma viral load &gt;1000 copies/mL. CNS measures included paired pre- vs post-ATI measures of mood, cognitive performance, and neurologic examination, with elective cerebrospinal fluid (CSF) sampling, brain diffusion tensor imaging (DTI) and magnetic resonance spectroscopy (MRS).ResultsMedian participant age was 30 years old and 29/30 were male. Participants’ median time on ART before ATI was 3 years, and ATI lasted a median of 35 days. Post-ATI, there were no differences in median mood scores or neurologic findings and cognitive performance improved modestly. During ATI, a low level of CSF HIV-1 RNA was detectable in 6 of 20 participants with plasma viremia, with no group changes in CSF immune activation markers or brain DTI measures. Mild worsening was identified in post-ATI basal ganglia total choline MRS, suggesting an alteration in neuronal membranes.ConclusionNo adverse CNS effects were observed with brief, closely monitored ATI in participants with acutely treated HIV, except an MRS alteration in basal ganglia choline. Further studies are needed to assess CNS ATI safety in HIV remission trials, particularly for studies using higher thresholds to restart ART and longer ATI durations.
Social Disadvantage, Politics, and Severe Acute Respiratory Syndrome Coronavirus 2 Trends: A County-level Analysis of United States Data
Authors: Mourad Ahmad , Turner Nicholas A , Baker Arthur W , Okeke Nwora Lance , Narayanasamy Shanti , Rolfe Robert , Engemann John J , Cox Gary M , Stout Jason E 
Published: September 2020

Abstract

Background
Understanding the epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for public health control efforts. Social, demographic, and political characteristics at the United States (US) county level might be associated with changes in SARS-CoV-2 case incidence.

Methods
We conducted a retrospective analysis of the relationship between the change in reported SARS-CoV-2 case counts at the US county level during 1 June–30 June 2020 and social, demographic, and political characteristics of the county.

Results
Of 3142 US counties, 1023 were included in the analysis: 678 (66.3%) had increasing and 345 (33.7%) nonincreasing SARS-CoV-2 case counts between 1 June and 30 June 2020. In bivariate analysis, counties with increasing case counts had a significantly higher Social Deprivation Index (median, 48 [interquartile range {IQR}, 24–72]) than counties with nonincreasing case counts (median, 40 [IQR, 19–66]; P = .009). Counties with increasing case counts were significantly more likely to be metropolitan areas of 250 000–1 million population (P &lt; .001), to have a higher percentage of black residents (9% vs 6%; P = .013), and to have voted for the Republican presidential candidate in 2016 by a ≥10-point margin (P = .044). In the multivariable model, metropolitan areas of 250 000–1 million population, higher percentage of black residents, and a ≥10-point Republican victory were independently associated with increasing case counts.

Conclusions
Increasing case counts of SARS-CoV-2 in the US during June 2020 were associated with a combination of sociodemographic and political factors. Addressing social disadvantage and differential belief systems that may correspond with political alignment will play a critical role in pandemic control.
Analysis on the Component Connectivity of Enhanced Hypercubes
Authors: Xu Liqiong , Guo Litao 
Published: September 2020

Abstract
Reliability evaluation of interconnection networks is of significant importance to the design and maintenance of interconnection networks. The component connectivity is an important parameter for the reliability evaluation of interconnection networks and is a generalization of the traditional connectivity. The $g$-component connectivity $c\kappa _g (G)$ of a non-complete connected graph $G$ is the minimum number of vertices whose deletion results in a graph with at least $g$ components. Determining the $g$-component connectivity is still an unsolved problem in many interconnection networks. Let $Q_{n,k}$ ($1\leq k\leq n-1$) denote the $(n, k)$-enhanced hypercube. In this paper, let $n\geq 7$ and $1\leq k \leq n-5$, we determine $c\kappa _{g}(Q_{n,k}) = g(n + 1) - \frac{1}{2}g(g + 1) + 1$ for $2 \leq g \leq n$. The previous result in Zhao and Yang (2019, Conditional connectivity of folded hypercubes. Discret. Appl. Math., 257, 388–392) is extended.
Honeycomb-like structure in spontaneous recanalized coronary thrombus demonstrated by serial angiograms: a case report
Authors: Kahata Mitsuru , Satomi Natsuko , Otsuka Masato , Ishii Yasuhiro 
Published: September 2020

Abstract

Background
The honeycomb-like structure (HLS) is a rare cause of myocardial ischaemia characterized by multiple communicating channels divided by thin septa. The aetiology of this specific structure remains speculative.

Case summary
A 55-year-old man was admitted due to worsening effort angina during the previous 2 months. Diagnostic coronary angiography revealed occlusion of the distal right coronary artery (RCA) with good collateral flow from the left coronary artery. We considered this lesion as a recent total occlusion, and planned a percutaneous coronary intervention (PCI). At the time of PCI, 7 days after admission, an angiogram showed a spontaneous recanalization of the occlusive RCA. Intravascular ultrasound (IVUS) depicted a HLS at the recanalized lesion, including atherosclerotic stenosis. We managed these lesions with drug-eluting stents.

Discussion
A recanalized thrombus may manifest as a HLS. In this case, the patient suffered from worsening effort angina during the previous 2 months, we confirmed a spontaneous recanalization of the occluded coronary lesion by serial angiographic images, and observed HLS adjacent to the atherosclerotic attenuated plaque by using high-resolution IVUS. Recanalized organizing thrombus is considered an entity of HLS. However, all previous studies on the HLS in vivo have detected the structure in an already recanalized state. Therefore, the aetiology remained speculative and evidence has been indirect. This present case demonstrates that recanalized atherosclerotic thrombosis might be one of the causes of HLS.
A case report of generalized lymphangiomatosis with chylopericardium: the crucial role of magnetic resonance lymphangiography
Authors: Mi Honglan , Chi Jiachang , Zhao Xiaojing , Lu Qing 
Published: September 2020

Abstract

Background
Chylopericardium due to generalized lymphangiomatosis is a rare clinical entity. Its aetiology and treatment remain unclear.

Case summary
We report one case of a 51-year-old man who was diagnosed with generalized lymphangiomatosis with idiopathic chylopericardium by bilateral inguinal intranodal contrast-enhanced magnetic resonance lymphangiography. Magnetic resonance lymphangiography demonstrated abnormal communications between the pericardial sac and the thoracic duct. The patient with idiopathic chylopericardium was therefore successfully treated by exclusive surgical ligation of the abnormal communications and partial pericardiectomy by thoracotomy. The patient’s postoperative recovery was uneventful, and no recurrence of pericardial effusion occurred during the 13-month follow-up.

Discussion
Magnetic resonance lymphangiography showed a good capability for evaluating the extent of generalized lymphangiomatosis and therefore is helpful for delineating the anatomy of the thoracic duct and identifying chyle leakage and abnormal communications between the thoracic duct and the pericardial sac. This makes a simple ligature of the abnormal communications, instead of thoracic duct mass ligation possible in the treatment of chylopericardium.