bluuebunny/crossref_metadata_2025_split huggingface dataset:
A flexible cross-platform single-cell data processing pipeline
Authors: Battenberg Kai , Kelly S. Thomas , Ras Radu Abu , Hetherington Nicola A. , Hayashi Makoto , Minoda Aki 
Published: November 2022

AbstractSingle-cell RNA-sequencing analysis to quantify the RNA molecules in individual cells has become popular, as it can obtain a large amount of information from each experiment. We introduce UniverSC (https://github.com/minoda-lab/universc), a universal single-cell RNA-seq data processing tool that supports any unique molecular identifier-based platform. Our command-line tool, docker image, and containerised graphical application enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms. We also provide a cross-platform application to run UniverSC via a graphical user interface, available for macOS, Windows, and Linux Ubuntu, negating one of the bottlenecks with single-cell RNA-seq analysis that is data processing for researchers who are not bioinformatically proficient.
An electrochemical biosensor for the rapid genetic identification of Musang King durian
Authors: Azizi Mohammad Malek Faizal , Romeli Sohana , Razali Hazana , Ariffin Eda Yuhana , Tajol Ariffin Muhammad Afiq , Heng Lee Yook , Abu-Bakar Norliza , Lau Han Yih 
Published: November 2022

AbstractMore than 200 different cultivars of durian exist worldwide but Durio zibethinus or Musang King (MK) is the most premium and prized durian fruit among the recommended varieties. Early identification of this premium variety is critical to protect from non-authentic MK durian cultivars. However, the MK variety's morphological traits are nearly identical to other varieties. Currently, the identification of durian varieties is mostly performed via evaluation of leaf shape, fruit shape, aroma, taste and seed shape and this requires trained personnel for the morphology observation. To enable the rapid identification of the MK variety, PCR amplification of ten durian varieties using six gene candidates from the chloroplast genome was first performed to obtain DNA probes that were specific to the MK durian variety. PCR amplification of ten durian varieties using primers designed confirmed that the nadhA gene sequence showed an obvious difference in the MK variety from other durian varieties. The unique sequence of MK was used as a DNA probe to develop an electrochemical biosensor for the direct identification of the MK durian variety. The electrochemical biosensor was based on the hybridization response of the immobilized DNA probe with the target DNA from the MK variety and was monitored via differential pulse voltammetry technique. Under optimal conditions, the DNA electrochemical biosensor showed a low detection limit at 10% of MK genomic DNA concentration with a wide linear calibration range of 0.05–1.5 µM (R2 = 0.9891) and RSD value of 3.77% (n = 3). The results of the developed DNA biosensor provide high promise for the development of portable sensors employed in the determination of MK variety in the field.
Oxidative stress mediates end-organ damage in a novel model of acetaminophen-toxicity in Drosophila
Authors: Saeedi Bejan J. , Hunter-Chang Sarah , Luo Liping , Li Kaiyan , Liu Ken H. , Robinson Brian S. 
Published: November 2022

AbstractAcetaminophen is the most common cause of acute drug-induced liver injury in the United States. However, research into the mechanisms of acetaminophen toxicity and the development of novel therapeutics is hampered by the lack of robust, reproducible, and cost-effective model systems. Herein, we characterize a novel Drosophila-based model of acetaminophen toxicity. We demonstrate that acetaminophen treatment of Drosophila results in similar pathophysiologic alterations as those observed in mammalian systems, including a robust production of reactive oxygen species, depletion of glutathione, and dose-dependent mortality. Moreover, these effects are concentrated in the Drosophila fat body, an organ analogous to the mammalian liver. Utilizing this system, we interrogated the influence of environmental factors on acetaminophen toxicity which has proven difficult in vertebrate models due to cost and inter-individual variability. We find that both increasing age and microbial depletion sensitize Drosophila to acetaminophen toxicity. These environmental influences both alter oxidative stress response pathways in metazoans. Indeed, genetic and pharmacologic manipulations of the antioxidant response modify acetaminophen toxicity in our model. Taken together, these data demonstrate the feasibility of Drosophila for the study of acetaminophen toxicity, bringing with it an ease of genetic and microbiome manipulation, high-throughput screening, and availability of transgenic animals.
Amoxicillin impact on pathophysiology induced by short term high salt diet in mice
Authors: Kumar Suresh , Perumal Nagarajan , Yadav P. K. , Pandey Ramendra Pati , Chang Chung-Ming , Raj V. Samuel 
Published: November 2022

AbstractCurrent evidence emerging from both human and animal models confirms that high-salt diet consumption over a period modulates the gut ecology and subsequently accelerates the development of the pathophysiology of many metabolic diseases. The knowledge of short-term intake of a high-salt diet (HSD) on gut microbiota and their role in the progression of metabolic pathogenesis and the consequence of a typical course of common antibiotics in this condition has yet not been investigated. The present study elicited this knowledge gap by studying how the gut microbiota profile changes in mice receiving HSD for a short period followed by Amoxicillin treatment on these mice in the last week to mimic a typical treatment course of antibiotics. In this study, we provided a standard chow diet (CD) and HSD for 3 weeks, and a subset of these mice on both diets received antibiotic therapy with Amoxicillin in the 3rd week. We measured the body weight of mice for 3 weeks. After 21 days, all animals were euthanised and subjected to a thorough examination for haemato-biochemical, histopathological, and 16S rRNA sequencing, followed by bioinformatics analysis to determine any changes in gut microbiota ecology. HSD exposure in mice for short duration even leads to a significant difference in the gut ecology with enrichment of specific gut microbiota crucially linked to developing the pathophysiological features of metabolic disease-related inflammation. In addition, HSD treatment showed a negative impact on haemato-biochemical parameters. However, Amoxicillin treatment in HSD-fed mice restored the blood-biochemical markers near to control values and reshaped gut microbiota known for improving the pathophysiological attributes of metabolic disease related inflammation. This study also observed minimal and insignificant pathological changes in the heart, liver, and kidney in HSD-fed mice.
Differentially expressed long noncoding RNAs and mRNAs in PC12 cells under lysophosphatidylcholine stimulation
Authors: Zhang Wen , Dun Su , Ping Yin , Wang Qingliang , Tana Siqin , Tana Aodong , Qin Si , Bao Xilinqiqige , Qimuge Alateng , Baiyin Tegexi , Yang Dezhi , Bao Siqin , Baoyin Seyin , Qimuge Wuhan 
Published: November 2022

AbstractLysophosphatidylcholine (LPC) was previously found to show neuroprotective effect on nerve growth factor (NGF) and brain derived neurotrophic factor (BDNF) induced signalings. Also, numerous studies reported the emerging roles of long noncoding RNAs (LncRNAs) involved in neurodegenerative disease. However, the biological mechanism of LPC and expression profile of lncRNAs has not been reported. Here, lncRNAs in PC12 cells under LPC and NGF treatment were analyzed using high throughput sequencing technology for the first time. We identified 564 annotated and 1077 novel lncRNAs in PC12 cells. Among them, 121 lncRNAs were differentially expressed in the PC12 cells under LPC stimulation. KEGG analysis showed that differentially expressed mRNAs co-expressed with lncRNAs mainly enriched in ribosome, oxidative phosphorylation, Parkinson’s disease, Huntington’s disease and Alzheimer’s disease etc. LncRNA-mRNA network analysis showed that lncRNA ENSRNOT00000082515 had interactions with 626 different mRNAs suggesting that lncRNA ENSRNOT00000082515 probably play vital role. Finally, sequencing data were validated by qRT-PCR for ENSRNOT00000084874, ENSRNOT00000082515, LNC_001033 forward Fgf18, Vcam1, and Pck2.
Caloric restriction improves glycaemic control without reducing plasma branched-chain amino acids or keto-acids in obese men
Authors: Sayda M. H. , Abdul Aziz M. H. , Gharahdaghi N. , Wilkinson D. J. , Greenhaff P. L. , Phillips B. E. , Smith K. , Idris I. , Atherton P. J. 
Published: November 2022

AbstractHigher plasma leucine, isoleucine and valine (BCAA) concentrations are associated with diabetes, obesity and insulin resistance (IR). Here, we evaluated the effects of 6-weeks very-low calorie diet (VLCD) upon fasting BCAA in overweight (OW) non-diabetic men, to explore associations between circulating BCAA and IR, before and after a weight loss intervention. Fasting plasma BCAAs were quantified in an OW (n = 26; BMI 32.4 ± 3 kg/m2; mean age 44 ± 9 y) and a normal-weight (NW) group (n = 26; BMI 24 ± 3.1 kg/m2; mean age 32 ± 12.3 y). Ten of the OW group (BMI 32.2 ± 4 kg/m2; 46 ± 8 y) then underwent 6-weeks of VLCD (600–800 kcal/day). Fasting plasma BCAA (gas chromatography-mass spectrometry), insulin sensitivity (HOMA-IR) and body-composition (DXA) were assessed before and after VLCD. Total BCAA were higher in OW individuals (sum leucine/isoleucine/valine: 457 ± 85 µM) compared to NW control individuals (365 ± 78 µM,p < 0.001). Despite significant weight loss (baseline 103.9 ± 12.3 to 93 ± 9.6 kg and BMI 32.2 ± 4 to 28.9 ± 3.6 kg/m2), no changes were observed in BCAAs after 6-weeks of VLCD. Moreover, although VLCD resulted in a significant reduction in HOMA-IR (baseline 1.19 ± 0.62 to 0.51 ± 0.21 post-VLCD;p < 0.001), Pearson’s r revealed no relationships between BCAA and HOMA-IR, either before (leucine R2: 2.49e−005,p = 0.98; isoleucine R2: 1.211−e006,p = 0.9; valine R2: 0.004,p = 0.85) or after VLCD (leucine R2: 0.003,p = 0.86; isoleucine R2: 0.006,p = 0.82; valine R2: 0.002,p = 0.65). Plasma BCAA are higher in OW compared to NW individuals. However, while 6-weeks VLCD reduced body weight and IR in OW individuals, this was not associated with reductions in BCAA. This suggests that studies demonstrating links between BCAA and insulin resistance in OW individuals, are complex and are not normalised by simply losing weight.
An open-source LED array illumination system for automated multiwell plate cell culture photodynamic therapy experiments
Authors: Zhang Kai , Timilsina Sudip , Waguespack Matthew , Kercher Eric M. , Spring Bryan Q. 
Published: November 2022

AbstractPhotodynamic therapy (PDT) research would benefit from an automated, low-cost, and easy-to-use cell culture light treatment setup capable of illuminating multiple well replicates within standard multiwell plate formats. We present an LED-array suitable for performing high-throughput cell culture PDT experiments. The setup features a water-cooling loop to keep the LED-array temperature nearly constant, thus stabilizing the output power and spectrum. The setup also features two custom-made actuator arms, in combination with a pulse-width-modulation (PWM) technique, to achieve programmable and automatic light exposures for PDT. The setup operates at ~ 690 nm (676–702 nm, spectral output full-width half-maximum) and the array module can be readily adapted to other LED wavelengths. This system provides an illumination field with adjustable irradiance up to 400 mW/cm2with relatively high spectral and power stability comparing with previously reported LED-based setups. The light doses provided by the LED array were validated with comparison to traditional laser PDT. This open-source illumination platform (including the detailed technical description, fabrication protocols, and parts list provided here) helps to make custom light sources more accessible and of practical use for photomedicine research.
The effect of negative pressures on the superconductivity of amorphous and crystalline bismuth
Authors: Quiroga Flor B. , Hinojosa-Romero David , Valladares Alexander , Valladares Renela M. , Rodríguez Isaías , Valladares Ariel A. 
Published: November 2022

AbstractMaterials may behave in non-expected ways when subject to unexpected conditions. For example, when Bi was turned into an amorphous phase (a-Bi) unexpectedly it became a superconductor at temperatures below 10 K. Using the superconductivity of the amorphous phase we provided an explanation as to why crystalline bismuth (c-Bi) had not been found to superconduct, and even predicted an upper limit for its superconducting transition temperature Tc. This was experimentally corroborated within the following year. We now decided to investigate what happens to the crystalline, Wyckoff structure, and amorphous Bi when pressures below the atmospheric are applied. Here it is shown that, within the BCS approach, under expansion the Wyckoff c-Bi increases its superconducting transition temperature minimally, whereas the amorphous phase decreases its Tc. The electron densities of states (eDoS), the vibrational densities of states (vDoS) and the Debye temperatures (θD) are calculated to perform this qualitative evaluation. Expansion can be obtained in the laboratory by chemically etching Bi-based alloys, for example, a process also known as dealloying.
Effect of print parameters on additive manufacturing of metallic parts: performance and sustainability aspects
Authors: Fongsamootr Thongchai , Thawon Itthidet , Tippayawong Nakorn , Tippayawong Korrakot Yaibuathet , Suttakul Pana 
Published: November 2022

AbstractIn this study, the effects of print parameters on the mechanical properties of additively manufactured metallic parts were investigated using a tensile test. The 17-4 PH stainless steel specimens with two print parameters, including infill density and pattern orientation, were fabricated by additive manufacturing (AM) using the bound metal deposition (BMD) technique. The mechanical properties considered in this study are the Young’s modulus and ultimate tensile strength. The results demonstrate that the pattern orientations do not affect the Young’s modulus of the infill specimen with the triangular pattern. In contrast, the ultimate strength significantly varies depending on the pattern orientations, where the samples with the pattern orientation of zero degrees yield the best ultimate strength. In fact, the mechanical properties of infill specimens increase with their infill density. However, when operating cost and time are considered, an index for estimating performance and sustainability is consequently established. The relationship between the normalized ultimate strength of an infill specimen and the relative density is defined as the weight efficiency. The index for assessing a sustainable product is characterized by the weight efficiency versus sustainable parameter(s). The index can help end users select an appropriate infill density for AM products by considering the operating cost and time. Different cost models, including material-only costs, direct costs, and total costs, can be included in the index model to assess a sustainable product in a particular cost context.
The fate of terrestrial biodiversity during an oceanic island volcanic eruption
Authors: Nogales Manuel , Guerrero-Campos María , Boulesteix Thomas , Taquet Noémie , Beierkuhnlein Carl , Campion Robin , Fajardo Silvia , Zurita Nieves , Arechavaleta Manuel , García Rafael , Weiser Frank , Medina Félix M. 
Published: November 2022

AbstractVolcanic activity provides a unique opportunity to study the ecological responses of organisms to catastrophic environmental destruction as an essential driver of biodiversity change on islands. However, despite this great scientific interest, no study of the biodiversity at an erupting volcano has yet been undertaken. On La Palma (Canary archipelago), we quantified the main species affected and their fate during the 85-day eruption (September–December 2021). Our main objective consisted of monitoring the biodiversity subjected to critical stress during this volcanic eruption. We found that all biodiversity within a 2.5 km radius was severely affected after the first two weeks. It is challenging to assess whether volcanism can drive evolutionary traits of insular organisms. Examples are the adaptation of an endemic conifer to high temperatures, selection of functional plant types—secondary woodiness—, effects of the disappearance of invertebrates and their influence in trophic nets and vertebrate trophic plasticity. However, our data suggest that such previous evolutionary changes might continue to favour their resilience during this eruption. Lastly, it is a very good opportunity to assess the extent to which these periodic volcanic catastrophes may constitute temporary windows of repeated opportunities for the evolution and speciation of oceanic island biota.
A randomized controlled trial of Baduanjin exercise to reduce the risk of atherosclerotic cardiovascular disease in patients with prediabetes
Authors: Ma Xiaojun , Li Manlin , Liu Lin , Lei Fenfang , Wang Liduo , Xiao Wenyan , Tan Yingzi , He Binghua , Ruan Sijie 
Published: November 2022

AbstractTo investigate the effectiveness of long-term Baduanjin and aerobic training on the 10-year risk of atherosclerotic cardiovascular disease in prediabetic patients. This study was single-blind randomized controlled trial. A total of 98 participants with prediabetes were randomly divided into three groups: the BDJ (n = 34), AT (n = 32), and control (n = 32) groups. Participants in the BDJ and AT groups underwent one year of supervised group exercise, consisting of 60 min/session every other day. The primary outcomes were metabolic control and the 10-year risk of ASCVD. The secondary outcome was a change in blood glucose status. After the intervention, various metabolic indexes were significantly improved in the two exercise groups relative to the control group and baseline measurements (p < 0.05). Compared with no exercise, BDJ and AT had significant preventive and protective effects against the risk of ASCVD in patients with prediabetes (p < 0.001). The overall effects of the two exercise groups were similar (p > 0.05). Long-term BDJ training can effectively reduce the risk of type 2 diabetes mellitus (T2DM) and its cardiovascular complications in prediabetic patients. The effect of BDJ is similar to that of moderate-intensity aerobic exercise.
Burden of diseases and injuries attributable to alcohol consumption in the Middle East and North Africa region, 1990–2019
Authors: Safiri Saeid , Nejadghaderi Seyed Aria , Noori Maryam , Sullman Mark J. M. , Collins Gary S. , Kaufman Jay S. , Kolahi Ali-Asghar 
Published: November 2022

AbstractAlcohol consumption is associated with a number of diseases and injuries, including cardiovascular diseases, cancers, mental and neurological disorders, as well as transport-related injuries. This article reports the alcohol-attributable burden of diseases and injuries at the regional and national levels in the Middle East and North Africa (MENA) region between 1990 and 2019, by sex, age, underlying cause, and Socio-demographic Index (SDI). The regional deaths and disability-adjusted life-years (DALYs) attributable to alcohol consumption were reported for the MENA region, between 1990 and 2019, using the methodological framework and analytical strategies adopted by the Global Burden of Disease (GBD) study 2019. The estimates were all reported as counts, population-attributable fractions, and age-standardised rates per 100,000 population, along with their corresponding 95% uncertainty intervals (UIs). Also, the average annual percentage changes were used to represent the trends of age-standardised rates. In 2019, there were an estimated 22.0 thousand deaths (95% UI: 16.1–29.4) and 1.1 million DALYs (0.8–1.3) attributable to alcohol consumption in the MENA region. The number of DALYs attributable to alcohol consumption were much higher in men (878.0 thousand, 691.4–1104.8) than among women (181.8, 138.6–232.0). The overall age-standardised death and DALY rates attributable to alcohol consumption decreased by 34.5% (13.2–48.3) and 31.9% (16.9–42.5), respectively, over the study period. Egypt (10.1 [5.7–16.6]) and Kuwait (1.1 [0.8–1.5]) had the highest and lowest age-standardised death rates attributable to alcohol consumption, respectively. In 2019, the number of deaths and DALYs in the MENA region were highest in those aged 60–64 and 50–54 years, respectively. A negative association was observed between a country’s SDI and their corresponding age-standardised DALY rates over the period 1990 to 2019. Digestive diseases were the main contributor to the alcohol-attributable burden. Over 1990–2019, the regional deaths and DALYs of diseases and injuries attributable to alcohol consumption decreased with AAPC of − 1.45 (− 1.78 to − 1.12) and − 1.31 (− 1.46 to − 1.15), respectively. The death and DALY rates attributable to alcohol consumption in the MENA region have decreased over the past three decades. Further decreases can be facilitated by implementing country-level policies and increasing public awareness.
Effective field of view of wide-field fundus photography in the Stanford University Network for Diagnosis of Retinopathy of Prematurity (SUNDROP)
Authors: Ji Marco H. , Zaidi Moosa , Bodnar Zachary , Wang Sean K. , Kumm Jochen , Moshfeghi Darius M. 
Published: November 2022

AbstractFive-field 130° wide-angle imaging is the standard of care for retinopathy of prematurity (ROP) screening with an ideal hypothetical composite field-of-view (FOV) of 180°. We hypothesized that in many real-world scenarios the effective composite FOV is considerably less than ideal. This observational retrospective study analyzed the effective FOV of fundus photos of patients screened for ROP as part of the Stanford University Network for Diagnosis of Retinopathy of Prematurity (SUNDROP) initiative. Five fundus photos were selected from each eye per image session. Effective FOV was defined as the largest circular area centered on the optic disc that encompassed retina in each of the four cardinal views. Seventy-three subjects were analyzed, 35 without ROP and 34 with ROP. Mean effective FOV was 144.55 ± 6.62° ranging from 130.00 to 153.71°. Effective FOV was not correlated with the presence or absence of ROP, gestational age, birth weight, or postmenstrual age. Mean effective FOV was wider in males compared to females. Standard five-field 130° fundus photos yielded an average effective FOV of 144.54° in the SUNDROP cohort. This implies that an imaging FOV during ROP screening considerably less than the hypothetical ideal of 180° is sufficient for detecting treatment warranted ROP.