bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust and scalable barcoding for massively parallel long-read sequencing
Authors: Ezpeleta Joaquín , Garcia Labari Ignacio , Villanova Gabriela Vanina , Bulacio Pilar , Lavista-Llanos Sofía , Posner Victoria , Krsticevic Flavia , Arranz Silvia , Tapia Elizabeth 
Published: May 2022

AbstractNucleic-acid barcoding is an enabling technique for many applications, but its use remains limited in emerging long-read sequencing technologies with intrinsically low raw accuracy. Here, we apply so-called NS-watermark barcodes, whose error correction capability was previously validated in silico, in a proof of concept where we synthesize 3840 NS-watermark barcodes and use them to asymmetrically tag and simultaneously sequence amplicons from two evolutionarily distant species (namelyBordetella pertussisandDrosophila mojavensis) on the ONT MinION platform. To our knowledge, this is the largest number of distinct, non-random tags ever sequenced in parallel and the first report of microarray-based synthesis as a source for large oligonucleotide pools for barcoding. We recovered the identity of more than 86% of the barcodes, with a crosstalk rate of 0.17% (i.e., one misassignment every 584 reads). This falls in the range of the index hopping rate of established, high-accuracy Illumina sequencing, despite the increased number of tags and the relatively low accuracy of both microarray-based synthesis and long-read sequencing. The robustness of NS-watermark barcodes, together with their scalable design and compatibility with low-cost massive synthesis, makes them promising for present and future sequencing applications requiring massive labeling, such as long-read single-cell RNA-Seq.
A non-canonical Raf function is required for dorsal–ventral patterning during Drosophila embryogenesis
Authors: Lusk Jay B. , Chua Ellora Hui Zhen , Kaur Prameet , Sung Isabelle Chiao Han , Lim Wen Kin , Lam Vanessa Yuk Man , Harmston Nathan , Tolwinski Nicholas S. 
Published: May 2022

AbstractProper embryonic development requires directional axes to pattern cells into embryonic structures. In Drosophila, spatially discrete expression of transcription factors determines the anterior to posterior organization of the early embryo, while the Toll and TGFβ signalling pathways determine the early dorsal to ventral pattern. Embryonic MAPK/ERK signaling contributes to both anterior to posterior patterning in the terminal regions and to dorsal to ventral patterning during oogenesis and embryonic stages. Here we describe a novel loss of function mutation in the Raf kinase gene, which leads to loss of ventral cell fates as seen through the loss of the ventral furrow, the absence of Dorsal/NFκB nuclear localization, the absence of mesoderm determinants Twist and Snail, and the expansion of TGFβ. Gene expression analysis showed cells adopting ectodermal fates much like loss of Toll signaling. Our results combine novel mutants, live imaging, optogenetics and transcriptomics to establish a novel role for Raf, that appears to be independent of the MAPK cascade, in embryonic patterning.
Assessing influences of climate change on highland barley productivity in the Qinghai-Tibet Plateau during 1978–2017
Authors: Zhang Zemin , Lu Changhe 
Published: May 2022

AbstractGrain production is becoming increasingly vulnerable to climate change globally. Highland barley (HB) is the most important cereal crop in the Qinghai-Tibet Plateau (QTP), so assessing HB productivity and its response to climate change could help to understand the capacity of grain production and food security. This study simulated the potential yield of HB annually at 72 meteorological stations for 1978–2017 using the WOFOST model, and then analyzed the spatiotemporal changes of HB potential yield and climatic factors in the growing season. Further, the influence of climate change on HB potential yield was explored in different temperature zones (TZ). Results indicate that the annual average of HB potential yield ranged from 3.5 to 8.1 t/ha in the QTP, and it was averaged at 6.5 t/ha in TZ-3, higher than other zones. From 1978 to 2017, HB potential yield for the whole QTP decreased slightly by 2.1 kg/ha per year, and its change rates were 23.9, 10.1, − 15.9, − 23.8 and − 16.7 kg/ha/year from TZ-1 to TZ-5 (p < 0.05), respectively. In all zones, average (Tave), maximum (Tmax) and minimum temperature (Tmin) showed a significantly warming trend (p < 0.01), and Tmin increased by 0.53, 0.45, 0.44, 0.40 and 0.69 °C per decade, higher than that of Tave and Tmax. However, temperature diurnal range (TDR) and radiation (RA) showed a downward trend, and their decrease rates were far higher in TZ-5 and TZ-3. In TZ-1, ΔTDR was the critical factor to the change in HB potential yield, which would increase by 420.30 kg/ha for 1 °C increase of ΔTDR (p < 0.01). From TZ-2 to TZ-5, ΔRA was the critical factor, but the influence amplitude in terms of the elastic coefficient, decreased from 4.08 to 0.99 (p < 0.01). In addition, other factors such as ΔTmax in TZ-3 and ΔTmin in TZ-4 and TZ-5 also had an important influence on the potential yield. To improve the HB productivity in the QTP, suitable varieties should be developed and introduced to adapt the climate warming in different temperature zones. In addition, efforts are needed to adjust the strategies of fertilizers and irrigation applications.
Pollen-mediated transfer of herbicide resistance between johnsongrass (Sorghum halepense) biotypes
Authors: Maity Aniruddha , Young Blake , Subramanian Nithya , Bagavathiannan Muthukumar 
Published: May 2022

AbstractJohnsongrass (Sorghum halepense) is a troublesome weed in row crop production in the United States. Herbicide resistance is a growing concern in this species, with resistance to ACCase-, ALS-, and EPSPS-inhibitors already reported. Pollen-mediated gene flow (PMGF) is capable of spreading herbicide resistance, but the extent of PMGF has not yet been studied in johnsongrass. Field experiments were conducted in a Nelder-wheel design to quantify the distance and frequency of PMGF from ALS-inhibitor-resistant (AR) to -susceptible (AS) johnsongrass across three environments (summer 2018, fall 2018, and fall 2019). The AR biotype (pollen donor) was established at the center of the wheel (5-m diameter), and a naturally occurring johnsongrass (AS) infestation was utilized as the pollen recipient, in eight directions and at nine distances (5, 10, 15, 20, 25, 35, 40, 45, and 50 m) within each direction. Seeds collected from the AS plants in each distance and direction were screened for survival to the ALS-inhibitor herbicide nicosulfuron (Accent Q) at 95 g ai ha−1under greenhouse conditions. The survivors (i.e. hybrids) were further confirmed based on the presence of the Trp574Leu mutation. At the closest distance of 5 m, PMGF was 9.6–16.2% across the directions and environments, which progressively declined to 0.8–1.2% at 50 m. The exponential decay model predicted 50% reduction in PMGF at 2.2 m and 90% reduction at 5.8 m from the pollen donor block. Results demonstrate that herbicide resistance can spread between adjacent field populations of johnsongrass through PMGF, which necessitates sound monitoring and management.
The biomechanical fundamentals of crosslink-augmentation in posterior spinal instrumentation
Authors: Cornaz Frédéric , Fasser Marie-Rosa , Snedeker Jess Gerrit , Spirig José Miguel , Farshad Mazda , Widmer Jonas 
Published: May 2022

AbstractPosterior screw-rod constructs can be used to stabilize spinal segments; however, the stiffness is not absolute, and some motion can persist. While the effect of crosslink-augmentation has been evaluated in multiple studies, the fundamental explanation of their effectiveness has not been investigated. The aim of this study was to quantify the parameters “screw rotation” and “parallelogram deformation” in posterior instrumentations with and without crosslinks to analyze and explain their fundamental effect. Biomechanical testing of 15 posteriorly instrumented human spinal segments (Th10/11—L4/L5) was conducted in axial rotation, lateral bending, and flexion–extension with ± 7.5 Nm. Screw rotation and parallelogram deformation were compared for both configurations. Parallelogram deformation occurred predominantly during axial rotation (2.6°) and was reduced by 60% (−1.45°, p = 0.02) by the addition of a crosslink. Simultaneously, screw rotation (0.56°) was reduced by 48% (−0.27°, p = 0.02) in this loading condition. During lateral bending, 0.38° of parallelogram deformation and 1.44° of screw rotation was measured and no significant reduction was achieved by crosslink-augmentation (8%, −0.03°, −p = 0.3 and −13%, −0.19°, p = 0.7 respectively). During flexion–extension, parallelogram deformation was 0.4° and screw rotation was 0.39° and crosslink-augmentation had no significant effect on these values (−0.12°, −30%, p = 0.5 and −0°, −0%, p = 0.8 respectively). In axial rotation, crosslink-augmentation can reduce parallelogram deformation and with that, screw rotation. In lateral bending and flexion–extension parallelogram deformation is minimal and crosslink-augmentation has no significant effect. Since the relatively large screw rotation in lateral bending is not caused by parallelogram deformation, crosslink-augmentation is no adequate countermeasure. The fundamental understanding of the biomechanical effect of crosslink-augmentation helps better understand its potential and limitations in increasing construct stiffness.
A two-sample Mendelian randomization analysis of modifiable risk factors and intracranial aneurysms
Authors: Tian Danyang , Zhang Linjing , Zhuang Zhenhuang , Huang Tao , Fan Dongsheng 
Published: May 2022

AbstractWe aimed to investigate the causality between potentially modifiable risk factors and the risk of intracranial aneurysm. Genetic instruments for 51 modifiable factors and intracranial aneurysm data were obtained from recently published genome-wide association studies. We applied two-sample Mendelian randomization methods to investigate their causal relationships. Genetically predicted cigarettes per day, smoking initiation, systolic blood pressure, hypertension and body fat percentage were significantly associated with an increased risk of intracranial aneurysm [odds ratios (OR) 2.67, 95% confidence interval (CI) 1.75–4.07, p = 5.36 × 10–6, OR 1.53, 95% CI 1.32–1.77, p = 9.58 × 10–9, OR 1.05, 95% CI 1.02–1.08, p = 1.18 × 10–3, OR 1.65, 95% CI 1.19–2.28, p = 2.56 × 10–3 and OR 1.29, 95% CI 1.11–1.52, p = 1.33 × 10–3, respectively]. Type 2 diabetes mellitus was significantly associated with a decreased risk of intracranial aneurysm (OR 0.89, 95% CI 0.83–0.95, p = 8.54 × 10–4). Body fat percentage was significantly associated with subarachnoid haemorrhage (p = 5.70 × 10–5). This study provided genetic evidence of causal effects of smoking, blood pressure, type 2 diabetes mellitus and obesity on the risk of intracranial aneurysm.
Prominence of the training data preparation in geomagnetic storm prediction using deep neural networks
Authors: Cristoforetti M. , Battiston R. , Gobbi A. , Iuppa R. , Piersanti M. 
Published: May 2022

AbstractThe direct interaction between large-scale interplanetary disturbances emitted from the Sun and the Earth’s magnetosphere can lead to geomagnetic storms representing the most severe space weather events. In general, the geomagnetic activity is measured by the Dst index. Consequently, its accurate prediction represents one of the main subjects in space weather studies. In this scenario, we try to predict the Dst index during quiet and disturbed geomagnetic conditions using the interplanetary magnetic field and the solar wind parameters. To accomplish this task, we analyzed the response of a newly developed neural network using interplanetary parameters as inputs. We strongly demonstrated that the training procedure strictly changes the capability of giving correct forecasting of stormy and disturbed geomagnetic periods. Indeed, the strategy proposed for creating datasets for training and validation plays a fundamental role in guaranteeing good performances of the proposed neural network architecture.
Impact of salivary and pancreatic amylase gene copy numbers on diabetes, obesity, and functional profiles of microbiome in Northern Japanese population
Authors: Hasegawa Takanori , Kakuta Masanori , Yamaguchi Rui , Sato Noriaki , Mikami Tatsuya , Murashita Koichi , Nakaji Shigeyuki , Itoh Ken , Imoto Seiya 
Published: May 2022

AbstractAmylase genes reside in a structurally complex locus, and their copy numbers vary greatly, and several studies have reported their association with obesity. The mechanism of this effect was partially explained by changes in the oral and gut microbiome compositions; however, a detailed mechanism has been unclarified. In this study, we showed their association with diabetes in addition to obesity, and further discovered a plausible mechanism of this association based on the function of commensal bacteria. First, we confirmed that the amylase copy number in the population tends to be larger than that reported in other studies and that there is a positive association between obesity and diabetes (p = 1.89E–2 and 8.63E–3). Second, we identified that relative abundance of some genus level microbiome, Capnocytophaga, Dialister, and previously reported bacteria, were significantly associated with amylase copy numbers. Finally, through functional gene-set analysis using shotgun sequencing, we observed that the abundance of genes in the Acarbose pathway in the gut microbiome was significantly decreased with an increase in the amylase copy number (p-value = 5.80E–4). Our findings can partly explain the mechanism underlying obesity and diabetes in populations with high amylase copy numbers.
Prognostic significance of cachexia index in patients with advanced hepatocellular carcinoma treated with systemic chemotherapy
Authors: Goh Myung Ji , Kang Wonseok , Jeong Woo Kyoung , Sinn Dong Hyun , Gwak Geum-Youn , Paik Yong-Han , Choi Moon Seok , Lee Joon Hyeok , Koh Kwang Cheol , Paik Seung Woon 
Published: May 2022

AbstractCancer cachexia affects quality of life, response to chemotherapy, and survival in many advanced cancer patients. The aim of this study was to evaluate the prognostic value of pretreatment cachexia index (CXI) in patients with advanced hepatocellular carcinoma (HCC) treated with systematic chemotherapy. Patients with advanced HCC treated with lenvatinib therapy between October 2018 and October 2020 were retrospectively studied. The CXI was calculated as (L3 skeletal muscle index) × (serum albumin)/(neutrophil-to-lymphocyte ratio). The association with treatment response and early adverse events within the first two months of lenvatinib therapy was investigated. Overall survival (OS) and progression-free survival (PFS) were estimated using the Kaplan–Meier method with log-rank test. Multivariable Cox regression was used to identify the predictors of survival. A total of 116 patients (median age: 60, male: 84.5% ) with calculated CXI. They divided into two groups: high CXI (≥ 53, n = 82) and low CXI (< 53, n = 34). Patients with low CXI had a significantly lower disease control rate (61.8% vs. 89.0%, p = 0.001) and a shorter median OS (8.0 [95% CI 6.2–9.8] vs. 12.3 [95% CI 10.1–14.4] months, p = 0.002) than those with high CXI. In multivariable analysis, low CXI was independently associated with shorter OS (HR: 2.07, 95% CI: 1.17–3.65, p = 0.01) and PFS (HR: 1.84, 95% CI: 1.09–3.09, p = 0.02). Of note, during the first two months of lenvatinib therapy, anorexia (41.2% vs. 22.0%, p = 0.04) developed more frequently among patients with low CXI than those with high CXI. The CXI may be a clinically useful index for predicting poor treatment response and prognosis in patients with advanced HCC undergoing lenvatinib treatment.
Effect of drought on root exudates from Quercus petraea and enzymatic activity of soil
Authors: Staszel Karolina , Lasota Jarosław , Błońska Ewa 
Published: May 2022

AbstractRoot exudation is a key process that determines rhizosphere functions and plant-soil relationships. The present study was conducted with the objectives to (1) determine the root morphology of sessile oak seedlings in relation to drought, (2) assess root exudation and its response to drought, and (3) detect possible changes in the activity of soil enzymes in response to drought enhancement. In the experiment, sessile oak seedlings (Quercus petraea Matt.) were used, and two variants of substrate moisture (25% humidity—dry variant and 55% humidity—fresh variant) on which oaks grew were considered. Exudates were collected using a culture-based cuvette system. Results confirmed the importance of drought in shaping the morphology of roots and root carbon exudation of sessile oak. The oak roots in the dry variant responded with a higher increment in length. In the case of roots growing in higher humidity, a higher specific root area and specific root length were determined. Experimental evidence has demonstrated decreased root exudation under dry conditions, which can lead to a change in enzyme activity. In the study, enzyme activity decreased by 90% for β-D-cellobiosidase (CB), 50% for β-glucosidase (BG) and N-acetyl-β-D-glucosaminidase (NAG), 20% for β-xylosidase (XYL) decreased by, and the activity of arylsulphatase (SP) and phosphatase (PH) decreased by 10%.
Optimization of chamfer masks using Farey sequences and kernel dimensionality
Authors: Maiseli Baraka Jacob 
Published: May 2022

AbstractFarey sequences have captured the attention of several researchers because of their wide applications in polygonal approximation, generation of Ford circles, and shape analysis. In this work, we extend the applications of these sequences to optimize chamfer masks for computation of distance maps in images. Compared with previous methods, the proposed method can more effectively generate optimal weights from larger chamfer masks without considering multiple and rather complex defining variables of the masks. Furthermore, our work demonstrates the relationship between size of the chamfer kernel, Farey sequence, and optimal weights of the chamfer mask. This interesting relationship, which may be useful in various image processing and computer vision tasks, has never been revealed by any other previous study. Results from the current research may advance our understanding on the applications of Farey sequences in computational geometry and vision-related tasks. To allow reproducibility of the results, implementation codes and datasets can be accessed in the public repository athttps://www.mathworks.com/matlabcentral/fileexchange/71652-optimization-of-chamfer-masks.
Bilateral subthalamic nucleus deep brain stimulation for refractory isolated cervical dystonia
Authors: Yin Feng , Zhao Mingming , Yan Xin , Li Tong , Chen Hui , Li Jianguang , Cao Shouming , Guo Hui , Liu Shuang 
Published: May 2022

AbstractSubthalamic nucleus (STN) deep brain stimulation (DBS) has been proven to be an alternative target choice for refractory isolated cervical dystonia (CD). However, assessments of its short and long-term safety, efficacy, and sustained effectiveness have been limited to few reports. Here, we evaluated nine consecutive refractory isolated CD patients who underwent bilateral STN DBS and accepted to short and long-term follow-up in this retrospective study. Seven time points were used to see the Toronto Western Spasmodic Torticollis Rating Scale (TWSTRS) scores (pre-operation [baseline], 1, 3, 6, 12, 24 months post-operation and last follow-up) to assess improvement of dystonic symptoms. The 36-item Short-Form General Health Survey (SF-36) scores obtained at pre-operation and last follow-up to assess the changes in quality of life. All patients tolerated surgery well and acquired observable clinical benefits from STN DBS therapy. All patients achieved a considerable improvement in quality of life at the last follow-up. The hardware-related adverse events can be tolerated and the stimulation-related adverse events can be ameliorated by programming. Our data support the idea that bilateral STN DBS is a safety and effective method for the treatment of refractory isolated CD, with persistent and remarkable improvement in both movement and quality of life.
The prevalence of acute stress disorder after acute myocardial infarction and its psychosocial risk factors among young and middle-aged patients
Authors: Wu Minjuan , Wang Wenqin , Zhang Xingwei , Li Junhua 
Published: May 2022

AbstractYoung and middle-aged people are vulnerable to developing acute stress disorder (ASD) following acute myocardial infarction (AMI). This study aims to explore the factors that contribute to ASD in young and middle-aged AMI patients. 190 AMI patients aged 18 to 60 years were enrolled in this study. We assessed the association between ASD and demographic data, adult attachment, and social support. This study examined a total of 190 young and middle-aged people. Among them, 65 participants were diagnosed with ASD, representing a 34.21% positive rate. Multivariate stepwise regression showed that adult attachment, infarct-related artery, social support, in-hospital complications are the main factors affecting ASD. Path analysis showed that social support had mediated the relationship between adult attachment and ASD. The incidence of ASD in young and middle-aged patients with AMI is high. Social support plays an important role in adult attachment and ASD relationships. Adult attachment and social support should be incorporated into post-traumatic cardiac rehabilitation to help patients cope with traumatic occurrences.
Prevalence of anxiety and depressive symptoms in ulcerative colitis patients in Jordan and its relationship to patient-reported disease activity
Authors: Abu Sneineh Awni , Haj Ali Sara , Al-Masri Ahmad , Diab Amr , Aldweik Farah , Darweesh Mohammad , Qaisi Mohammad , Alshakhatreh Osama , Tamimi Tarek , Rayyan Yaser , Banimustafa Radwan , Sablaban Ibrahim 
Published: May 2022

AbstractInflammatory bowel disease is associated with higher rates of anxiety and depression compared to the general population. We aimed to determine the prevalence of anxiety and depressive symptoms among patients with ulcerative colitis and correlation to disease activity. In this cross-sectional study, we collected data from 70 consecutive ulcerative colitis patients over one year at our inflammatory bowel disease outpatient clinic through an interview and a questionnaire containing patient demographics and disease characteristics. Anxiety and depressive symptoms were characterized using the Generalized Anxiety Disorder-7 questionnaire and Patient Health Questionnaire-9, respectively, with ulcerative colitis disease severity assessed by the Partial Mayo scoring system. The majority of our patients were females (68.6%) and the mean age was 39.3 years. Rates of anxiety and depressive symptoms among ulcerative colitis patients were 65.7% and 58.6%, respectively. Depressive symptoms were significantly associated with patient-reported disease activity (r = 0.361; p = 0.010). Significant percentages of ulcerative colitis patients were appreciated to have anxiety and depressive symptoms, and there was a correlation between patient-reported disease activity and depressive symptoms. At this high rate of prevalence, it is justified to screen patients for the presence of psychiatric comorbidities.