bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpretation of Morphological Details of Nondegenerated Lumbar Intervertebral Discs on Magnetic Resonance Imaging: Insights From a Comparison Between Computed Tomography Discograms and Magnetic Resonance Imaging
Authors: Sharma Aseem , Lagerstrand Kerstin , Brisby Helena , Hebelka Hanna 
Published: March 2022

Objective
To gain better insight into the magnetic resonance imaging (MRI) appearance of morphological intervertebral disc (IVD) details, such as annular and nucleus pulposus dimensions, by comparing contemporaneously obtained MRI and postdiscogram computed tomography (CT) scans of nondegenerated IVDs.

Methods
Axial T2-weighted images and same-day postdiscography CTs, acquired after the MRI, of 26 normal-appearing lumbar IVDs (control IVDs at discography) were compared. The location and extent of central hyperintense zone on MRI and the extent of contrast distribution on CT relative to the IVD width (in anteroposterior [AP] and lateral planes) were assessed, with difference in measures between the modalities used to provide apparent inner annulus thickness and to estimate dimensions of also the outer annulus and location of nucleus pulposus.

Results
The mean (SD) extent of contrast distribution on CT discograms (53.1% [6.6%] and 58.1% [8.7%] of AP and lateral IVD width) was smaller than (P < 0.001 for both), and correlated weakly (r = 0.31 and 0.32 for AP and lateral planes) with corresponding measurements (58.4% [5.3%] and 65.7% [5.9%], respectively) for central hyperintense zone at MRI. The center of contrast opacification on CT discograms was located posterior to that of central T2 hyperintense zone on MRI in AP (P < 0.01), without any difference in lateral direction (P = 0.60).

Conclusions
Normal-appearing lumbar IVDs are supported by outer annulus of larger relative thickness anteriorly, seen on both modalities. The shown discrepancy between the central T2 hyperintense zone and contrast distribution on CT discogram might reflect the inner annulus or structural changes within the borderzone nucleus and annulus. The exact nucleus size and inner annulus thickness could not be established due to a variable permeation of contrast across the central hyperintense zone on T2-weighted images.
Anodal Stimulation Latency Response Differences Between Ipsilateral and Contralateral Motor Evoked Potentials in Hand Muscles
Authors: Gonzalez Andres A. , Mahani Tandis , Parikh Pooja 
Published: March 2022

Purpose:
Purpose of this study was to analyze the latency and amplitude of transcranial motor evoked potentials responses from the contralateral and ipsilateral muscle groups to the same stimulus. If responses are because of activation of deeper structures, the latency of both the ipsilateral and the contralateral responses should have no difference. However, a difference in latency would suggest that activation might be occurring at different subcortical levels.

Methods:
Data regarding demographics, medical history, and neurophysiological parameters were collected retrospectively on patients undergoing lumbar spine surgeries. Each side transcranial MEPs was considered as an independent data. Latency and amplitude of motor responses were recorded from the hand muscles of the ipsilateral and contralateral side from the same transcranial stimulus at preincision baseline. Statistical data analysis was performed using SAS 9.4. Paired t test was used to identify mean of differences in latency and amplitude between contralateral and ipsilateral intrinsic hand muscle.

Results:
Data on 54 patients (104 MEPs) were obtained. Using paired t test, mean of differences in latency between ipsilateral (crossover) and contralateral (desired) intrinsic hand muscle was 0.8967 milliseconds (P < 0.0001) while median was 0.71 milliseconds. Using paired t test, mean of differences in amplitude between ipsilateral and contralateral hand muscles was −1,071 µV (P = <0.0001).

Conclusions:
Significant latency differences were seen between the contralateral and the ipsilateral hand MEP responses using the same transcranial stimulus, suggesting a different subcortical activation. Understanding of this difference might help better in the selection of baselines, and whether to favor responses obtained under the anode or under the cathode.
Comparing Machine Learning Architectures for the Prediction of Peptide Collisional Cross Section
Authors: Franklin Emily , Röst Hannes L. 
Published: March 2022

1AbstractMass spectrometry is the method of choice in large-scale proteomics studies. One common method is data-independent acquisition (DIA), which allows for high-throughput analysis of biological samples, but also produces complex data. Methods of peptide separation, in addition to retention time, improve data analysis and there has been increasing interest in separating peptides based on collisional cross section (CCS), which is a measure of the size of a peptide. However, existing libraries that are used during data analysis lack CCS measurements, and this data is expensive and time-consuming to acquire. This has led to the desire to predict library values for mass spectrometry analysis. Here we compare three deep learning architectures, LSTM, CNN, and transformer, for the tasks of retention time and collisional cross section prediction. We show that the LSTM and CNN models perform similarly and that the transformer has a lower performance than expected.
Plant-associated fungi support bacterial resilience following water limitation
Authors: Hestrin Rachel , Kan Megan , Lafler Marissa , Wollard Jessica , Kimbrel Jeffrey A. , Ray Prasun , Blazewicz Steven , Stuart Rhona , Craven Kelly , Firestone Mary , Nuccio Erin , Pett-Ridge Jennifer 
Published: March 2022

AbstractDrought disrupts soil microbial activity and many biogeochemical processes. Although plant-associated fungi can support plant performance and nutrient cycling during drought, their effects on nearby drought-exposed soil microbial communities are not well resolved. We used H18O quantitative stable isotope probing (qSIP) and 16S rRNA gene profiling to investigate bacterial community dynamics following water limitation in the hyphospheres of two distinct fungal lineages (Rhizophagus irregularisandSerendipita bescii) grown with the bioenergy model grassPanicum hallii. In uninoculated soil, a history of water limitation resulted in significantly lower bacterial growth potential and growth efficiency, as well as lower diversity in the actively growing bacterial community. In contrast, both fungal lineages had a protective effect on hyphosphere bacterial communities exposed to water limitation: bacterial growth potential, growth efficiency, and the diversity of the actively growing bacterial community were not suppressed by a history of water limitation in soils inoculated with either fungus. Despite their similar effects at the community level, the two fungal lineages did elicit different taxon-specific responses, and bacterial growth potential was greater inR. irregularis- compared inS. bescii- inoculated soils. Several of the bacterial taxa that responded positively to fungal inocula belong to lineages that are considered drought-susceptible. Overall, H18O qSIP highlighted treatment effects on bacterial community structure that were less pronounced using traditional 16S rRNA gene profiling. Together, these results indicate that fungal-bacterial synergies may support bacterial resilience to moisture limitation.
Multimodal single-cell profiling of intrahepatic cholangiocarcinoma defines hyperactivated Tregs as a potential therapeutic target
Authors: Alvisi Giorgia , Termanini Alberto , Soldani Cristiana , Portale Federica , Carriero Roberta , Pilipow Karolina , Polidoro Michela , Franceschini Barbara , Malenica Ines , Puccio Simone , Lise Veronica , Galletti Giovanni , Zanon Veronica , Colombo Federico Simone , Tufano Michele , Aghemo Alessio , Di Tommaso Luca , Peano Clelia , Cibella Javier , Iannacone Matteo , Roychoudhuri Rahul , Donadon Matteo , Torzilli Guido , Kunderfranco Paolo , Di Mitri Diletta , Lugli Enrico , Lleo Ana 
Published: March 2022

AbstractThe quality of the immune infiltrate of intrahepatic cholangiocarcinoma (iCCA), a rare, yet aggressive tumor of the biliary tract, remains poorly characterized, limiting development of successful immunotherapies. We used high-dimensional flow cytometry to characterise the T cell and myeloid compartments of iCCA comparing these with their tumor-free peritumoral and circulating counterparts. We found poor infiltration of putative tumor-specific CD39+ CD8+ T cells accompanied by abundant infiltration of hyperactivated CD4+ regulatory T cells (Tregs), whose frequency in relation to that of CD4+ CD69+ T cells and conventional type 2 dendritic cells was associated with poor prognosis. Single-cell RNA-sequencing identified an altered network of transcription factors in iCCA-infiltrating compared to peritumoral T cells, suggesting reduced effector functions by tumor-infiltrating CD8+ T cells and enhanced immunosuppression by CD4+ Tregs. Specifically, we found that expression of mesenchyme homeobox 1 (MEOX1) was highly enriched in tumor-infiltrating Tregs, and demonstrated that MEOX1 overexpression is sufficient to reprogram circulating precursors to acquire the transcriptional and epigenetic landscape of tumorinfiltrating Tregs. Interfering with hyperactivated Tregs should be thus explored to enhance antitumor immunity in iCCA.
Predicting butyrate- and propionate-forming bacteria of gut microbiota from sequencing data
Authors: Kircher Berenike , Woltemate Sabrina , Gutzki Frank , Schlüter Dirk , Geffers Robert , Bähre Heike , Vital Marius 
Published: March 2022

AbstractBackgroundThe bacteria-derived short chain fatty acids (SCFAs) butyrate and propionate play important (distinct) roles in health and disease and understanding the ecology of respective bacteria on a community-wide level is a top priority in microbiome research. The aim of this study was to reveal members harboring main pathways for the production of those metabolites and assess the applicability of sequence data (metagenomics and 16S rRNA gene) to predict SCFAs production in vitro and in vivo.ResultsA clear split between butyrate- and propionate-forming bacteria was detected with only very few taxa exhibiting pathways for the production of both SCFAs. After in vitro growth of fecal communities from distinct donors (n=8) on different substrates (n=7) abundances of bacteria exhibiting pathways correlated with respective SCFA concentrations, in particular in the case of butyrate. While final growth differed markedly between cultures, communities showed high functional redundancies with comparable yields, i.e., concentration of metabolite per grown bacterium exhibiting pathway(s), irrespective of the donor and substrate used. For propionate, correlations were weaker indicating that its production is less imprinted into the core metabolism compared with butyrate-forming bacteria. Longitudinal measurements in vivo (five samples derived from 20 subjects) also revealed a correlation between abundances of pathway-carrying bacteria and concentrations of the two SCFAs. Additionally, lower bacterial cell concentrations, together with higher stool moisture, promoted overall bacterial activity (measured by flow cytometry and coverage patterns of metagenome-assembled genomes) that led to elevated SCFAs concentrations with over-proportional levels of butyrate. Butyrate concentrations displayed lower temporal stability than propionate, however, abundances of bacteria exhibiting the butyrate-forming pathway were more stable than those carrying pathways for propionate production. Predictions on pathway abundances based on 16S rRNA gene data using our in-house database worked well yielding similar results as metagenomic-based analyses.ConclusionsWe demonstrated that pathway abundances enable predictions on concentrations of SCFAs indicating that stimulating bacterial growth directly leads to more production of those compounds. The strong separation of gut microbiota into two functional communities facilitates the development of precision intervention strategies targeting either metabolite.
Putative SET-domain methyltransferases in Cryptosporidium parvum and histone methylation during infection
Authors: Sawant Manasi , Benamrouz-Vanneste Sadia , Meloni Dionigia , Gantois Nausicaa , Even Gaёl , Guyot Karine , Creusy Colette , Duval Erika , Wintjens René , Weitzman Jonathan , Chabe Magali , Viscogliosi Eric , Certad Gabriela 
Published: March 2022

AbstractCryptosporidium parvum is a major cause of an intestinal pathology called cryptosporidiosis which affects humans and other vertebrates. Despite being declared as a public health problem by World Health Organization (WHO) since 2006, pathogenesis caused by this parasite remains poorly understood. More recently, C. parvum has been linked with oncogenesis. In particular, the mechanisms involved in the processes of gene expression regulation are completely unexplored in Cryptosporidium. In the current study, we took the opportunity to investigate a dynamic epigenetic modification called histone lysine methylation during the life cycle of the parasite. We successfully identified putative SET-domain containing proteins, lysine methyltransferases (KMTs), which catalyze the methylation of different lysine residues. Phylogenetic analysis classified them into distinct subfamilies namely CpSET1, CpSET2, CpSET8, CpKMTox and CpAKMT. Structural analysis further characterized CpSET1, CpSET2 and CpSET8 to be histone lysine methyltransferases (HKMTs). Their functional significance was predicted by using site-specific methyl-lysine antibodies during development of the parasite (CpSET1:H3K4; CpSET2:H3K36; CpSET8:H4K20). In particular, the SET domain of CpSET8 showcased methyltransferase activity confirming the existence of functional HKMTs in Cryptosporidium. Moreover, the consequence of C. parvum infection on the host lysine methylation events highlights the inherit potential of the parasite to exploit the host epigenetic regulation to its advantage. Thus, this study is the first one to provide insights on epigenetics mechanisms occurring throughout the parasite’s life cycle and during the interaction with its host. As Cryptosporidium is a protozoan that significantly affects the health of both humans and animals, a better understanding of its developmental processes within the definitive host may highlight novel infection control strategies.Author SummaryCryptosporidium species have a very compact genome (~9.2 Mb) unlike its apicomplexan homologs such as Toxoplasma (~63 Mb). Moreover, the lack of large families of transcriptional factors requires them to heavily rely on chromatin remodeling components for its gene regulation. Thus, study and identification of novel elements which contribute to chromatin dynamics could assist a better understanding of the biology of this parasite. In the current study we investigated histone lysine methylation, a dynamic epigenetic modification which regulates gene activation as well as repression. More importantly, characterizing the enzymes which bring about this regulation, provides potential new druggable targets to attack the parasite.
A cadherin mutation in Celsr3 linked to Tourette Disorder affects dendritic patterning and excitability of cholinergic interneurons
Authors: Poppi Lauren A. , Ho-Nguyen K.T. , Wu Junbing , Matrongolo Matthew , Thackray Joshua K. , Nasello Cara , Shi Anna , Ricci Matthew , Carayannopoulos Nicolas L. , Cheedalla Nithisha , McGinnis Julianne , Schaper Samantha , Daut Cynthia , Hernandez Jurdiana , Heiman Gary A. , Tischfield Jay A. , Tischfield Max A. 
Published: March 2022

AbstractCELSR3 encodes an atypical protocadherin cell adhesion receptor that was recently identified as a high-risk gene for Tourette disorder. A putative damaging de novo variant was inserted into the mouse genome to generate an amino acid substitution within the fifth cadherin repeat. By contrast to Celsr3 constitutive null animals, mice homozygous for the R774H amino acid substitution are viable and have grossly normal forebrain development. The density of cortical and striatal interneuron subpopulations is normal, but 3D geometric analysis of cortical pyramidal neurons and striatal cholinergic interneurons revealed changes to dendritic patterning and types and distributions of spines. Furthermore, patch clamp recordings in cholinergic interneurons located within the sensorimotor striatum uncovered mild intrinsic hyperexcitability. Despite these changes, Celsr3R774H homozygous mice do not show obvious ‘tic-like’ stereotypies at baseline nor motor learning impairments, but females exhibited perseverative digging behavior. Our findings show that a human mutation in CELSR3 linked to Tourette disorder is sufficient to alter dendritic patterning in the cortex and striatum and also the intrinsic excitability of cholinergic interneurons.
Modeling of environmental effect factor and exergetic sustainability index with cuckoo search algorithm for a business jet
Authors: Oruc Ridvan , Baklacioglu Tolga , Turan Onder , Aydin Hakan 
Published: March 2022

Purpose
The purpose of this paper is to create models that predict exergetic sustainability index (ESI) and environmental effect factor (EEF) values with high accuracy according to various engine parameters.

Design/methodology/approach
In this study, models were created to estimate ESI and EEF sustainability parameters in various flight phases for a business jet with a turboprop engine using the cuckoo search algorithm (CSA) method. The database used for modeling includes the various engine parameters (torque, engine airflow, gas generator speed, fuel mass flow, power and air-fuel ratio) obtained by running a business aircraft engine more than once at different settings and the actual ESI and EEF values obtained depending on these parameters. In addition, sensitivity analysis was performed to measure the effect of engine parameters on the models. Finally, the effect of the CSA number of nest (n) parameter on the model accuracy was investigated.

Findings
It has been observed that the models predict ESI and EEF values with high accuracy. As a result of the sensitivity analysis, it was seen that the air-fuel ratio had a greater effect on the output parameters.

Practical implications
These models are thought to assist in the exergetic environment analysis used to find the greatest losses for turboprop business jets and identify their causes and further improve system performance. Thus, they will be a useful tool to minimize the negative impact of business jet on environmental sustainability.

Originality/value
To the best of the authors’ knowledge, this study stands out in the literature because it is the first exergo-metaheuristic approach developed with CSA for business aircraft engine; moreover, the data set used consists of real values.
Congruences modulo prime for fractional colour partition function
Authors: Rahman Riyajur , Saikia Nipen 
Published: March 2022

PurposeLet p[1,r;t] be defined by ∑n=0∞p[1,r;t](n)qn=(E1Er)t, where t is a non-zero rational number, r ≥ 1 is an integer and Er=∏n=0∞(1−qr(n+1)) for |q| < 1. The function p[1,r;t](n) is the generalisation of the two-colour partition function p[1,r;−1](n). In this paper, the authors prove some new congruences modulo odd prime ℓ by taking r = 5, 7, 11 and 13, and non-integral rational values of t.Design/methodology/approachUsing q-series expansion/identities, the authors established general congruence modulo prime number for two-colour partition function.FindingsIn the paper, the authors study congruence properties of two-colour partition function for fractional values. The authors also give some particular cases as examples.Originality/valueThe partition functions for fractional value is studied in 2019 by Chan and Wang for Ramanujan's general partition function and then extended by Xia and Zhu in 2020. In 2021, Baruah and Das also proved some congruences related to fractional partition functions previously investigated by Chan and Wang. In this sequel, some congruences are proved for two-colour partitions in this paper. The results presented in the paper are original.
Relational demography in organizations: an assessment of the explored and overlooked
Authors: Kaur Manpreet , Ren Hong 
Published: March 2022

PurposeThe study aims to present an in-depth review of previous research on relational demography (individual–team dissimilarity) over the past 30 years. In doing so, the authors highlighted the main theoretical underpinnings, teased out the common methodological approaches and identified the major mediating processes and contingency factors that influence relational demography's effect on individual outcomes in teams.Design/methodology/approachThe authors searched and examined eight databases (ABI/INFORM Complete, ProQuest, EBSCO, Web of Science, JSTOR, PsycARTICLES, PsycINFO and Science Direct) and distilled 106 studies from 34 journals. The authors synthesized and analyzed this body of work to identify extant patterns and themes in relational demography.FindingsThe findings reveal that the majority of theories used are categorized into three segments. The antecedents used are mainly surface- and deep-level variables, while the outcomes are classified into personal- and work-related constructs. For research testing, Euclidean distance and Blau's index are primarily utilized as heterogeneity measures, while various forms of regression are used as the analytical tool for hypotheses testing.Originality/valueExtant literature reviews on relational demography are scant. This study provides an extensive synthesis and analysis of the studies in the area over the past 30 years and offers an agenda that can motivate future research.
Performing indoor PM2.5prediction with low-cost data and machine learning
Authors: Lagesse Brent , Wang Shuoqi , Larson Timothy V. , Kim Amy Ahim 
Published: March 2022

PurposeThe paper aims to develop a particle matter (PM2.5) prediction model for open-plan office space using a variety of data sources. Monitoring of PM2.5levels is not widely applied in indoor settings. Many reliable methods of monitoring PM2.5require either time-consuming or expensive equipment, thus making PM2.5monitoring impractical for many settings. The goal of this paper is to identify possible low-cost, low-effort data sources that building managers can use in combination with machine learning (ML) models to approximate the performance of much more costly monitoring devices.Design/methodology/approachThis study identified a variety of data sources, including freely available, public data, data from low-cost sensors and data from expensive, high-quality sensors. This study examined a variety of neural network architectures, including traditional artificial neural networks, generalized recurrent neural networks and long short-term memory neural networks as candidates for the prediction model. The authors trained the selected predictive model using this data and identified data sources that can be cheaply combined to approximate more expensive data sources.FindingsThe paper identified combinations of free data sources such as building damper percentages and weather data and low-cost sensors such as Wi-Fi-based occupancy estimator or a Plantower PMS7003 sensor that perform nearly as well as predictions made based on nephelometer data.Originality/valueThis work demonstrates that by combining low-cost sensors and ML, indoor PM2.5monitoring can be performed at a drastically reduced cost with minimal error compared to more traditional approaches.