bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studies for searching factors relating rumination time around the heat season in Holstein milking cows
Authors: Seto Takahiro , Toba Yuichi 
Published: March 2022

AbstractTo identify factors affecting rumination time (RT), factorial analyses in a dairy farm were performed. In univariate analyses, differences in distribution were observed between low (< 45 kg/d) and high (≥ 45 kg/d) milk yield (MY) before the heat season, early and peak lactation periods and mid and late at the start of the heat season, and 1-2 and ≥ 3 parity at the start of the heat season. Multiple regression analysis confirmed that RT was affected by low MY, early to peak and 1-2 parity cows, low MY, mid to late and 1-2 parity cows, and low MY, early to peak and ≥ 3 parity cows (coefficients = −37.039, −25.353, −44.805 respectively,P< 0.05). When the cows were classified by MY before the heat season, the RT and MY of the high-MY group remained higher than the low-MY group until before the severe heat (THI ≥ 84 continued). However, when cows were classified by RT before the heat season, there was no difference in MY between the low-RT (< 485 min/d) and the high-RT group (> 485 min/d). In conclusions, MY is a factor affecting RT up to moderate heat but RT is not a sufficient condition affecting MY.
The Development of 2-stage Microfermentation Protocols for High Throughput Cell Factory Evaluations
Authors: Li Shuai , Ye Zhixia , Moreb Eirik A. , Menacho-Melgar Romel , Lynch Michael D. 
Published: March 2022

AbstractCell based factories can be engineered to produce a wide variety of products. Advances in DNA synthesis and genome editing have greatly simplified the design and construction of these factories. It has never been easier to generate hundreds or even thousands of cell factory strain variants for evaluation. These advances have amplified the need for standardized, higher throughput means of evaluating these designs. Toward this goal, we have previously reported the development of engineered E. coli strains and associated 2-stage production processes to simplify and standardize strain engineering, evaluation and scale up. This approach relies on decoupling growth (stage 1), from production, which occurs in stationary phase (stage 2). Phosphate depletion is used as the trigger to stop growth as well as induce heterologous expression. Here, we describe in detail the development of optimal protocols used for the evaluation of engineered E. coli strains in 2-stage microfermentations. These protocols are readily adaptable to the evaluation of strains producing a wide variety of protein as well as small molecule products. Additionally, the development approach described is adaptable to additional cellular hosts, as well as other 2-stage processes with various additional triggers.
Mucosal microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients
Authors: Tran Hoang N. H. , Hoang Thu Trang Nguyen , Nguyen Phu Huu , Vo Chi Nguyen , Van Doan Khanh , Ngoc Minh Chau Nguyen , Nguyen Ngoc Tuan , Duc Ta Van Ngoc , Vu Khuong An , Hua Thanh Danh , Thi Nguyen To Nguyen , Van Tan Trinh , Duc Trung Pham , Duong Ba Lap , Nguyen Phuc Minh , Hoang Vinh Chuc , Pham Duy Thanh , Thwaites Guy E. , Hall Lindsay J. , Slade Daniel J. , Baker Stephen , Tran Vinh Hung , The Hao Chung 
Published: March 2022

AbstractPerturbations in the gut microbiome have been linked to the promotion and prognosis of colorectal cancer (CRC), with the colonic overabundance of Fusobacterium nucleatum shown as the most consistent marker. Despite the increasing health burden inflicted by CRC in low- and middle-income countries like Vietnam, the CRC-specific microbiome in these populations remains underexplored. Here we conducted a study in Vietnam to enrol 43 CRC patients (cases) and 25 patients with non-cancerous colorectal polyps (controls) between December 2018 and January 2020. Our study investigated the mucosal microbiome signature and genomic diversity of Fusobacterium in Vietnamese CRC patients, using a combination of 16S rRNA gene profiling, anaerobic microbiology, and whole genome sequencing. We found that several oral bacteria, including F. nucleatum and Leptotrichia, were significantly more abundant in the tumour mucosa, and these two bacteria were also more enriched in tumours of advanced CRC stages (III-IV). We obtained 53 Fusobacterium genomes from the saliva, tumour and non-tumour mucosa of six CRC patients. Isolates from the gut mucosa belonged to diverse F. nucleatum subspecies (nucleatum, animalis, vincentii, polymorphum) and a potential new subspecies of F. periodonticum. The Fusobacterium population within each individual was distinct and in many cases diverse, with minimal intra-clonal variation. Phylogenetic analyses showed that within each individual, tumour-associated Fusobacterium were clonal to those isolated from non-tumour mucosa, but distantly related to those isolated from saliva. Genes encoding major virulence factors (Fap2 and RadD) showed variability in length and evidence of horizontal gene transfer. Our work provides a framework to understand the genomic diversity of Fusobacterium within the CRC patients, which can be exploited for the development of CRC diagnostic and therapeutic options targeting this oncobacterium.
Photizo: an open-source library for cross-sample analysis of FTIR spectroscopy data
Authors: Grant-Peters Melissa , Rich-Griffin Charlotte , Grant-Peters Jonathan E. , Cinque Gianfelice , Dendrou Calliope A. 
Published: March 2022

AbstractWith continually improved instrumentation, Fourier transform infrared (FTIR) microspectroscopy can now be used to capture thousands of high-resolution spectra for chemical characterisation of a sample. The spatially resolved nature of this method lends itself well to histological characterisation of complex biological specimens. However, commercial software currently available can make joint analysis of multiple samples challenging and, for large datasets, computationally infeasible. In order to overcome these limitations, we have developed Photizo - an open-source Python library for spectral analysis which includes functions for pre-processing, visualisation and downstream analysis, including principal component analysis, clustering, macromolecular quantification and biochemical mapping. This library can be used for analysis of spectroscopy data without a spatial component, as well as spatially-resolved data, such as data obtained via infrared (IR) microspectroscopy in scanning mode and IR imaging by focal plane array (FPA) detector.Contactcdendrou@well.ox.ac.uk
LabNet: hardware control software for the Raspberry Pi
Authors: Schatz Alexej , Winter York 
Published: March 2022

AbstractSingle-board computers such as the Raspberry Pi make it easy to control hardware setups for laboratory experiments. GPIOs and expansion boards (HATs) give access to a whole range of sensor and control hardware. However, controlling such hardware can be challenging, when many experimental setups run in parallel and the time component is critical. LabNet is a C++ optimized control layer software to give access to the Raspberry Pi connected hardware over a simple network protocol. LabNet was developed to be suitable for time-critical operations, and to be simple to expand. It leverages the actor model to simplify multithreading programming and to increase modularity. The message protocol is implemented in Protobuf and offers performance, small message size, and supports a large number of programming languages on the client side. It shows good performance compared to locally executed tools like Bpod or pyControl, outperforms Autopilot and reaches sub-millisecond range in network communication latencies. LabNet itself does not provide support for the design of experimental tasks. This is left to the client. LabNet can be used for general automation in experimental laboratories with its control PC located at some distance. LabNet is open source and under continuing development.
Dark kinase annotation, mining and visualization using the Protein Kinase Ontology
Authors: Soleymani Saber , Gravel Nathan , Huang Liang-Chin , Yeung Wayland , Bozorgi Elika , Bendzunas Nathaniel G. , Kochut Krzysztof J. , Kannan Natarajan 
Published: March 2022

ABSTRACTThe Protein Kinase Ontology (ProKinO) is an integrated knowledge graph that conceptualizes the complex relationships connecting protein kinase sequence, structure, function, and disease in a human and machine-readable format. Here we extend the scope of ProKinO as a discovery tool by including new classes and relationships capturing information on kinase ligand binding sites, expression patterns, and functional features, and demonstrate its application in uncovering new knowledge regarding understudied members of the protein kinase family. Specifically, through graph mining and aggregate SPARQL queries, we identify the p21-activated protein kinase 5 (PAK5) as one of the most frequently mutated dark kinase in human cancers with abnormal expression in multiple cancers, including an unappreciated role in acute myeloid leukemia. We identify recurrent oncogenic mutations in the PAK5 activation loop predicted to alter substrate binding and phosphorylation and identify common ligand/drug binding residues in PAK family kinases, highlighting the potential application of ProKinO in drug discovery. The updated ontology browser and a web component, ProtVista, which allows interactive mining of kinase sequence annotations in 3D structures and Alphafold models, provide a valuable resource for the signaling community. The updated ProKinO database is accessible athttp://prokino.uga.edu/browser/.
Flexible Control as Surrogate Reward or Dynamic Reward Maximization
Authors: Liljeholm Mimi 
Published: March 2022

AbstractThe utility of a given experience, like interacting with a particular friend or tasting a particular food, fluctuates continually according to homeostatic and hedonic principles. Consequently, to maximize reward, an individual must be able to escape or attain outcomes as preferences change, by switching between actions. Recent work on human and artificial intelligence has defined such flexible instrumental control in information theoretic terms and postulated that it may serve as a reward surrogate. Another possibility, however, is that the adaptability afforded by flexible control is tacitly implemented by planning for dynamic changes in outcome values. In the current study, an expected utility model that computes decision values over a range of possible monetary gains and losses associated with sensory outcomes provided the best fit to behavioral choice data and performed best in terms of earned rewards. Moreover, consistent with previous work on perceived control and personality, individual differences in dimensional schizotypy were correlated with behavioral choice preferences in conditions with the greatest and lowest levels of flexible control. These results contribute to a growing literature on the role of instrumental control in goal-directed choice.
Lower limb in sprinters with larger relative mass but not larger normalized moment of inertia
Authors: Sado Natsuki , Ichinose Hoshizora , Kawakami Yasuo 
Published: March 2022

AbstractPurposeSprinters exhibit inhomogeneous muscularity corresponding to musculoskeletal demand for sprinting execution. An inhomogeneous morphology would affect the mass distribution, which in turn may affect the mechanical difficulty in moving from an inertia perspective; however, the morphological characteristics of sprinters from the inertia perspective have not been examined. Here we show no corresponding differences in the normalized mass and normalized moment of inertia between the sprinters and untrained non-sprinters.MethodsWe analyzed fat- and water-separated magnetic resonance images from the lower limbs of 11 male sprinters (100 m best time of 10.44–10.83 s) and 12 untrained non-sprinters. We calculated the inertial properties by identifying the tissue of each voxel and combining the literature values for each tissue density.ResultsThe lower-limb relative mass was significantly larger in sprinters (18.7 ± 0.7% body mass) than in non-sprinters (17.6 ± 0.6% body mass), while the normalized moment of inertia of the lower limb around the hip in the anatomical position was not significantly different (0.044 ± 0.002 vs. 0.042 ± 0.002 [a. u.]). The thigh relative mass in sprinters (12.9 ± 0.4% body mass) was significantly larger than that in non-sprinters (11.9 ± 0.4% body mass), whereas the shank and foot relative masses were not significantly different.ConclusionWe revealed that the mechanical difficulty in swinging the lower limb is not relatively larger in sprinters in terms of inertia, even though the lower-limb mass is larger, reflecting their muscularity. We provide practical implications that sprinters can train without paying close attention to the increase in lower-limb mass and moment of inertia.
Japanese national well-being survey shows that living alone results in lower satisfaction and affects other relationships, while social networking service usage is related to life satisfaction: A cross-sectional study
Authors: Miyaki Koichi , Kawamura Takashi , Takano Hirohisa , Suzuki Kan Hiroshi 
Published: March 2022

AbstractThis study examined how social isolation and subjective loneliness impacted subjective well-being across Japan, with the aim of offering policy recommendations. We analyzed data (N = 5,234, age:15-89) obtained through a Japanese population-based national survey conducted in March 2021. First, we found that mean life satisfaction was statistically lowest among the subgroup of respondents who lived alone (approximately 20% of the total), with more pronounced impacts in males. We also found that the frequency of social networking site (SNS) usage was significantly associated with overall life satisfaction, exhibiting a J-curve (three to four times per week was better than everyday usage). The frequency of interaction with others, number of SNS friends, employment/wage satisfaction, family budget/asset satisfaction, subjective health satisfaction, and subjective connectedness were also related to well-being in a dose-dependent manner (Trend P<0.001). Second, our multiple logistic regression model showed that the above relationships were independently and statistically significant (p<0.05). Moreover, a stratified analysis showed that living alone significantly affected these relationships, which suggests that this condition should specifically be addressed in the context of efforts aimed at enhancing subjective well-being. In addition, respondents who lived alone had low subjective connectedness, which also independently influenced well-being, as shown by our multivariate logistic model. In sum, these findings indicate that national well-being enhancement policies should particularly consider social isolation and loneliness, including issues stemming from low social connectedness.
An Immunobridging study to evaluate the neutralizing antibody titer in adults immunized with two doses of either ChAdOx1-nCov-19 (AstraZeneca) or MVC-COV1901
Authors: Estrada Josue Antonio , Cheng Chien-Yu , Ku Shin-Yen , Hu Hui-Chun , Yeh Hsiu-Wen , Lin Yi-Chun , Chen Cheng-Pin , Cheng Shu-Hsing , Lin I-Feng 
Published: March 2022

AbstractBackgroundRapid development and deployment of vaccine is crucial to control the continuously evolving COVID-19 pandemic. Placebo-controlled phase 3 efficacy trial is still standard for authorizing vaccines in majority of the world. However, due to lack of cases or participants in parts of the world, this has not always been feasible. An alternative to efficacy trial is immunobridging, in which the immune response or correlates of protection of a vaccine candidate is compared against an approved vaccine. Here we describe a case study where our candidate vaccine, MVC-COV1901, has been granted for emergency use authorization (EUA) locally based on the non-inferiority immunobridging process.MethodsThe per protocol immunogenicity (PPI) subset from the MVC-COV1901 phase 2 trial was used for this study and consisted of 903 subjects who have received two doses of MVC-COV1901 as scheduled in the clinical trial. The comparator set of population consisted of 200 subjects of ≥ 20 years of age who were generally healthy and have received two doses of AstraZeneca ChAdOx nCOV-19 (AZD1222) recruited from Taoyuan General Hospital, Ministry of Health and Welfare.ResultsMVC-COV1901 was shown to have a geometric mean titer (GMT) ratio lower bound 95% confidence interval (CI) of 3.4 against the comparator vaccine and a seroconversion rate of 95.5% at the 95% CI lower bound, which both exceeded the criteria set by the Taiwan regulatory authority for EUA approval. These results supported the EUA approval of MVC-COV1901 by the Taiwanese regulatory authority in July 2021. Following the consensus of the International Coalition of Medicines Regulatory Authorities (ICMRA), countries from the Access Consortium has recently adopted the use of immunobridging studies as acceptable for authorizing COVID-19 vaccines in lieu of efficacy data.ConclusionThe data presented in the study showed that it is reasonably likely that the vaccine efficacy of MVC-COV1901 is similar or superior to that of AZ. Data could be used in support of further vaccine development and regulatory approval.
Optimal protocol design for diffusion-weighted imaging of the prostate: an estimation theory examination of parameter estimate variance
Authors: Conlin Christopher C , Seibert Tyler M , Dale Anders M 
Published: March 2022

AbstractDiffusion-weighted imaging (DWI) is routinely used to aid in the detection and characterization of prostate cancer. Given imaging time constraints in a clinical setting, it is important to maximize the statistical efficiency of a DWI examination of the prostate. The objective is to maximize the accuracy with which microstructural information about the prostate can be obtained while minimizing diffusion scan time.In this study, we apply estimation theory to evaluate the statistical efficiency of different DWI acquisitions and methods. Specifically, we show that the variance of DWI parameters estimated using nonlinear multiexponential signal models is considerably higher than the variance observed using linear signal models. We then derive a simple analytical expression for the efficiency of a linear estimator and use it to optimize b-value sampling for DWI of the prostate.
Converting cropping systems into seasonal habitat functionality reveals the hump-shaped responses of carabid beetles to agricultural management
Authors: Muneret Lucile , Ricci Benoit , Vialatte Aude , Aviron Stéphanie , Ducourtieux Chantal , Biju-Duval Luc , Petit Sandrine 
Published: March 2022

ABSTRACTUnderstanding effects on the huge diversity of cropping systems on local biodiversity is challenging but necessary to implement agroecological systems. Through a functional approach, the translation of cropping systems into resource and disturbance gradients is promising to decipher the relationship between cropping systems and biodiversity but has never been implemented for arthropods.To investigate contributions of resource and disturbance gradients arising from cropping systemsvsenvironmental context (regional effect, meteorological conditions and landscape characteristics) on beneficial arthropod communities, we used a dataset collected in 60 crop fields from three French areas over a five-years period. It includes all farmers interventions, crop sequences, meteorological data, landscape composition and carabid samplings.We found that the environmental context contributed to about 75% of explained carabid variations on average, while resource and disturbance gradients contributed to about 25% of explained carabid variations. The resource and disturbance gradients were particularly important in winter and spring preceding the spring-summer period to determine carabid variations.Moreover, we identified thresholds above which resource and disturbance gradients start being beneficial or detrimental for carabids. For example, a Treatment Frequency Index above 2.07 in spring decreased the total activity density of carabids during the spring-summer period.Synthesis and application. While implementing for the first time a functional approach to understand the effects of different facets of cropping systems on arthropods, our study also allows us to identify periods and thresholds above which specific practices affect carabids. The identification of such thresholds can guide the provision of recommendations for policy, stakeholders and farmers about how to reduce cropping systems’ impact on arthropods.
Environmental DNA reflects common haplotypic variation
Authors: Adams Clare I M , Hepburn Christopher , Jeunen Gert-Jan , Cross Hugh , Taylor Helen R , Gemmell Neil J , Bunce Michael , Knapp Michael 
Published: March 2022

AbstractAnalysis of environmental DNA (eDNA) has gained widespread usage for taxonomically based biodiversity assessment. While interest in applying non-invasive eDNA monitoring for population genetic assessments has grown, its usage in this sphere remains limited. One barrier to uptake is that the effectiveness of eDNA detection below the species level remains to be determined for multiple species and environments. Here, we test the utility of this emergent technology in a population genetic framework using eDNA samples derived from water along New Zealand’s South Island (Otago Coast: n=9; Kaikōura: n=7) and DNA obtained from tissue samples (n=76) of individual blackfoot pāua (Haliotis iris)sampled from New Zealand’s Otago coast. We recovered four mitochondrial haplotypes from eDNA versus six from the tissue samples collected. Three common haplotypes were recovered with both eDNA and tissue samples, while only one out of three rare haplotypes – represented in tissue samples by one individual each – was recovered with our eDNA methods. We demonstrate that eDNA monitoring is an effective tool for recovering common genetic diversity from pāua, although rare (< 5%) haplotypes are seldom recovered. Our results show the potential of eDNA to identify population-level haplotypes for gastropods in the marine environment identification below the species level and for studying the population genetic diversity of gastropods. This work supports eDNA methods as effective, non-invasive tools for genetic monitoring. Non-invasive eDNA sampling could minimize target organism stress and human interaction enabling population genetic research for hard-to-sample, delicate, or sensitive species.