bluuebunny/crossref_metadata_2025_split huggingface dataset:
“The Ties that Bind are those that Punish: Network Polarization and Federal Crime Policy Gridlock, 1979–2005”
Authors: Duxbury Scott W 
Published: April 2024

Abstract
Largely overlooked in research on criminal legal expansion is the rise of political polarization and its attendant consequences for crime policy. Drawing on theories of intergroup collaboration and policymaking research, I argue that network polarization—low frequencies of collaborative relations between lawmakers belonging to distinct political groups—negatively affects crime legislation passage by reducing information flows, increasing intergroup hostility, and creating opportunities for political attacks. To evaluate this perspective, I recreate dynamic legislative networks between 1979 and 2005 using data on 1,897,019 cosponsorship relationships between 1537 federal lawmakers and the outcomes of 5950 federal crime bills. Results illustrate that increases in partisan network segregation and the number of densely clustered subgroups both have negative effects on bill passage. These relationships are not moderated by majority party status and peak during the 1990s and early 2000s, a period when prison growth showed its first signs of slowing. These findings provide new insight to the relationship between polarization and policy and suggest that increases in network polarization may be partly responsible for declines in crime policy adoption observed in recent decades.
Study on factors contributing to severity of ship collision accidents in the Yangtze River estuary
Authors: Gao Xinjia , Dai Wei , Yu Lu , Yu Qifeng 
Published: April 2024

Abstract
The Yangtze River estuary in China is characterized by a complex maritime geographical environment and presents significant challenges to ship manoeuvring and control, thereby increasing the risk of ship collision accidents. Based on the 2013–2022 shipwreck investigation report published by Shanghai and Zhejiang Maritime Safety Administration, this paper analyses the primary factors responsible for ship collision accident severity in the Yangtze River estuary from four aspects, namely ship, environment, human and management. Utilizing accident severity as the dependent variable and 24 factors, including ship type, gross tonnage, wind speed, operational errors and so on, as independent variables, the study employed a stepwise regression approach to filter the variables. Subsequently, an ordered probit regression model was constructed based on the 10 most influential variables, followed by a marginal effect analysis. The findings indicate that a ship's gross tonnage, wind speed, ocean current speed, offshore distance and day/night conditions significantly influence the likelihood of different accident levels. Specifically, wind speed, offshore distance and ocean current speed have a negative impact on minor and general accidents while positively affecting major and severe accidents. Gross tonnage and daytime/nighttime have a positive impact on minor and general accidents but negatively impact major and severe accidents. Moreover, general accidents exhibit the most pronounced marginal effect for each explanatory variable. The findings can help the shipping authorities to identify the causes of ship collision accidents and take effective measures to reduce such accidents, thereby enhancing the safety of ship navigation in the area.
The relationship of vitamin D to the MHAQ index, activity disease, and inflammation in a sample of Syrian rheumatoid disease patients
Authors: Shahada Zienab , Kudsi Maysoun , Youssef Lama , Kabalan Younes 
Published: April 2024

Background:Vitamin D has an immunomodulatory and anti-inflammatory role, and its deficiency has been linked with many autoimmune disorders, including rheumatoid arthritis (RA). The correlation ship between the severity of RA and serum levels of vitamin D is a subject of immense interest and therapeutic implications.Patients and Methods:A total of 100 patients previously diagnosed with RA were collected from visitors to the rheumatology clinic at the university hospital and their ages were over 18 years. The serum vitamin D value and the C-reactive protein (CRP) value were measured, and the Disease Activity Score CRP28 (DAS28CRP) and Modified Health Assessment Questionnaire (MHAQ) score were calculated to determine the severity and effectiveness of the disease and its relationship to vitamin D deficiency.Results:The average age of the patients ranged according to the patient’s age (46.03±11.291), we note that individuals whose ages ranged from 26 to 65 accounted for the largest percentage (94%), 83% of women (83) and 17% men (17), and the mean score for sun exposure was 15.80±5.446. Patients were individuals diagnosed with the disease between 5 and 10 years were the highest group, with a percentage of 31%. A total of 72% of the patients were not treated with corticosteroids, and 43% of the patients were treated with vitamin D. We found that the number of patients using biologic medications was 18%, and the number of patients using disease-modifying anti-rheumatic drugs was 88%. The mean of DAS28 was moderate in 63% of patients, and the average of the MHAQ score was 0.80±0.334. We found that there is no statically significant correlation between the serum vitamin D level and DAS28/CRP (P=0.733), and there is also no statically significant correlation between the serum value of vitamin D and the medications used, whether biological or disease-modifying anti-rheumatic drugs (P=0.361). In addition, there is also no significant correlation between the serum vitamin D level and MHAQ score (P=0.100).Conclusion:There was no significant relationship between vitamin D deficiency and the disease activity or severity in a sample of patients with RA.
Adjusting Atrial Size Parameters for Body Surface Area
Authors: Kirkbride Rachael R. , Aviram Galit , Heidinger Benedikt H. , Liberman Yuval , Libauske Aurelija , Liubauskas Rokas , Tridente Daniela M. , Brook Alexander , DaBreo Dominique C. , Monteiro Filho Antonio C. , Carroll Brett J. , Matos Jason D. , McCormick Ian C. , Manning Warren J. , Litmanovich Diana E. 
Published: April 2024

Purpose:
Small left atrial (LA) volume was recently reported to be one of the best predictors of acute pulmonary embolism (PE)-related adverse events (AE). There is currently no data available regarding the impact that body surface area (BSA)-indexing of atrial measurements has on the association with PE-related adverse events. Our aim is to assess the impact of indexing atrial measurements to BSA on the association between computed tomography (CT) atrial measurements and AE.

Materials and Methods:
Retrospective study (IRB: 2015P000425). A database of hospitalized patients with acute PE diagnosed on CT pulmonary angiography (CTPA) between May 2007 and December 2014 was reviewed. Right and left atrial volume, largest axial area, and axial diameters were measured. Patients undergo both echocardiographies (from which the BSA was extracted) and CTPAs within 48 hours of the procedure. The patient’s body weight was measured during each admission. LA measurements were correlated to AE (defined as the need for advanced therapy or PE-related mortality at 30 days) before and after indexing for BSA. The area under the ROC curve was calculated to determine the predictive value of the atrial measurements in predicting AE.

Results:
The study included 490 acute PE patients; 62 (12.7%) had AE. There was a significant association of reduced BSA-indexed and non-indexed LA volume (both <0.001), area (<0.001 and 0.001, respectively), and short-axis diameters (both <0.001), and their respective RA/LA ratios (all <0.001) with AE. The AUC values were similar for BSA-indexed and non-indexed LA volume, diameters, and area with LA volume measurements being the best predictor of adverse outcomes (BSA-indexed AUC=0.68 and non-indexed AUC=0.66), followed by non-indexed LA short-axis diameter (indexed AUC=0.65, non-indexed AUC=0.64), and LA area (indexed AUC=0.64, non-indexed AUC=0.63).

Conclusion:
Adjusting for BSA does not substantially affect the predictive ability of atrial measurements on 30-day PE-related adverse events, and therefore, this adjustment is not necessary in clinical practice. While LA volume is the better predictor of AE, LA short-axis diameter has a similar predictive value and is more practical to perform clinically.
Improved Python Package for DNA Sequence Encoding using Frequency Chaos Game Representation
Authors: Halder Abhishek , Piyush  , Mathew Bernadette , Sengupta Debarka 
Published: April 2024

AbstractSummaryFrequency Chaos Game Representation (FCGR), an extended version of Chaos Game Representation (CGR), emerges as a robust strategy for DNA sequence encoding. The core principle of the CGR algorithm involves mapping a onedimensional sequence representation into a higher-dimensional space, typically in the two-dimensional spatial domain. This paper introduces a use case wherein FCGR serves as a kmer frequency-based encoding method for motif classification using a publicly available dataset.Availability and implementationThe FCGR python package, use case, along with additional functionalities, is available in theGitHub. Our FCGR package demonstrates superior accuracy and computational efficiency compared to a leading R-based FCGR library [1], which is designed for versatile tasks, including proteins, letters, and amino acids with user-defined resolution. Nevertheless, it is important to note that our Python package is specifically designed for DNA sequence encoding, where the resolution is predetermined based on the kmer length. It is a drawback of our current package compared to the state-of-the-art R-based kaos package [1].
Planar Optical Tweezer Trap (2D-LOT) System Realized by Light Sheet Illumination & Orthogonal Widefield Detection
Authors: Baro Neptune , Mondal Partha Pratim 
Published: April 2024

We report the realization of the first planar optical tweezer trap system by a sheet of light. To visualize the trapping of the target object (dielectric bead or live cell) in a plane, an orthogonal widefield detection is employed. The planar / two-dimensional lightsheet optical tweezer (2D-LOT) sub-system is realized in an inverted microscopy mode with illumination from the bottom. A 1064 nm laser (power ∼ 500mW) is expanded and directed to a combination of cylindrical lens and high NA objective lens to generate a tightly-focused diffraction-limited light sheet. The object to be trapped is injected in the specimen chamber (consists of two coverslips placed at a distance of ≈ 1mm) using a syringe. The solution containing the objects stayed in the chamber due to the surface tension of the fluid. The illumination of trap-laser light is along Z-direction (with coverslip along XZ-plane) whereas, the detection is achieved perpendicular to the coverslip (along Y-axis). The orthogonal detection is employed to directly visualize the trapping in a plane. To better visualize the specimen, a separate white light illumination sub-system is used. The characterization of system PSF estimates the size of light sheet trap PSF to be, 2073.84µm2which defines the active trap region / area. Beads are tracked on their way to the trap region for determining the trap stiffness along Z and X i.e,kz= 1.13 ± 0.034pN/µmandkx= 0.74±0.021pN/µm. Results (image and video) show real-time trapping of dielectric beads in the trap zone (2D plane) generated by the light sheet. The beads can be seen getting trapped from all directions in the XZ-plane. Prolonged exposure to the light sheet builds up a 2D array of beads in the trap zone. Similar experiments on live NIH3T3 cells show cells trapped in the 2D trap. The potential of the planar trap lies in its ability to confine objects in two dimensions, thereby opening new kinds of experiments in biophysics, atomic physics, and optical physics.Statement of SignificanceThe ability to trap and confine objects in two dimensions / a plane is an incredible feat that paves the way for new experiments in physical and biological sciences. Currently, no technique can achieve two-dimensional trapping of objects. Such a trap is realized by a sheet of light generating a near-rectangular potential trap-zone, enabling tweezing confined to a plane. This is unlike existing point-focus-based tweezers that are capable of point-potential well. The technique is expected to have widespread applications in science and engineering.
Integrating Transmission Dynamics and Pathogen Evolution Through a Bayesian Approach
Authors: Stolz Ugnė , Stadler Tanja , Vaughan Timothy G. 
Published: April 2024

AbstractThe collection of pathogen samples and subsequent genetic sequencing enables the reconstruction of phylogenies, shedding light on transmission dynamics. However, many existing phylogenetic methods fall short by neglecting within-host diversity and the impact of transmission bottlenecks, leading to inaccuracies in understanding epidemic spread. This paper introduces theTransmission Tree (TnT)model, which leverages multiple pathogen gene trees to more accurately model transmission history. By extending the Bayesian phylogenetic analysis softwareBEAST2, TnTintegrates the sampled ancestor birth-death model for transmission trees and the multi- species coalescent model for pathogen gene trees. This integration allows for the consideration of critical factors like transmission orientation, incomplete lineage sorting, and within- and between-host diversity. Notably,TnTincorporates an analytical approach to address unobserved transmission events, crucial in scenarios with incomplete sampling. Through theoretical evaluation and application to real-world cases like HIV transmission chains, we demonstrate thatTnToffers a robust solution to improve understanding of epidemic dynamics by effectively combining pathogen gene sequences and clinical data.
Arabidopsis WALL-ASSOCIATED KINASES are not required for oligogalacturonide-induced signaling and immunity
Authors: Herold Laura , Hua Chenlei , Kohorn Bruce , Nürnberger Thorsten , DeFalco Thomas , Zipfel Cyril 
Published: April 2024

AbstractCarbohydrate-based cell wall signaling impacts plant growth, development, and stress responses; however, how cell wall signals are perceived and transduced remains poorly understood. Several cell wall breakdown products have been described as typical damage-associated molecular patterns (DAMPs) that activate plant immunity, including pectin-derived oligogalacturonides (OGs). Receptor kinases (RKs) of the WALL-ASSOCIATED KINASE (WAK) family have been shown to bind pectin and OGs, and were previously proposed as OG receptors. However, unambiguous genetic evidence for the role of WAKs in OG responses is lacking. Here, we investigated the role of Arabidopsis WAKs in OG perception using a novel deletion mutant of the clusteredWAKfamily. Using a combination of immune assays for early and late pattern-triggered immunity (PTI), we show that WAKs are dispensable for OG-induced signaling and immunity, indicating that they are notbona fideOG receptors.
Sex-based difference in immune responses and efficacy of the pneumococcal conjugate vaccine
Authors: Tchalla Essi Y. I. , Betadpur Anagha , Khalil Andrew Y. , Bhalla Manmeet , Bou Ghanem Elsa N. 
Published: April 2024

AbstractVaccine-mediated protection and susceptibility toStreptococcus pneumoniae(pneumococcus) infections are influenced by biological sex. The incidence of invasive pneumococcal disease remains higher in males compared to females even after the introduction of the pneumococcal conjugate vaccine (PCV). However, sex-based differences in the immune response to this conjugate vaccine remain unexplored. To investigate those differences, we vaccinated adult male and female mice with PCV and assessed cellular and humoral immune responses. Compared to females, male mice displayed lower levels of T follicular helper cells, germinal center B cells and plasmablasts, which are all required for antibody production following vaccination. This was linked to lower IgG and IgM levels against pneumococci and lower isotype switching to IgG3 in vaccinated males. Additionally, sera of vaccinated male mice had lower efficacy in several anti-pneumococcal functions including neutralization of bacterial binding to pulmonary epithelial cells as well as direct cytotoxicity againstS. pneumoniae. Importantly, while the vaccine was highly protective in females, vaccinated males succumbed to infection more readily and were more susceptible to both lung-localized infection and systemic spread followingS. pneumoniaechallenge. These findings identify sex-based differences in immune responses to PCV that can inform future vaccine strategies.
Muscle-fiber specific genetic manipulation of Drosophila sallimus severely impacts neuromuscular development, morphology, and physiology
Authors: Michael Andrew H. , Hana Tadros A. , Mousa Veronika G. , Ormerod Kiel G. 
Published: April 2024

AbstractThe ability of skeletal muscles to contract is derived from the unique genes and proteins expressed within muscles, most notably myofilaments and elastic proteins. Here we investigated the role of the sallimus (sls) gene, which encodes a structural homologue of titin, in regulating development, structure, and function ofDrosophila melanogaster. Ubiquitous knockdown ofslsusing RNA interference (RNAi) in all muscle fibers resulted in embryonic lethality. A screen for muscle-specific drivers revealed a Gal4 line that expresses in a single larval body wall muscle in each abdominal hemisegment. Disruptingslsexpression in single muscle fibers did not impact egg or larval viability nor gross larval morphology, but did significantly alter the morphology of individual muscle fibers. Analysis of individual sarcomeres revealed significant changes in ultrastructural organization, dramatically increasing sarcomere, I-band, A-band, andsls-band lengths. Surprisingly, muscle-cell specific disruption ofslsalso severely impacted neuromuscular junction (NMJ) formation. The extent of motor-neuron (MN) innervation along disrupted muscles was significantly reduced along with the number of glutamatergic boutons, in MN-Is and MN-Ib. Electrophysiological recordings revealed a 40% reduction in excitatory junctional potentials correlating with the extent of motor neuron loss. Analysis of active zone (AZ) composition revealed changes in presynaptic scaffolding protein (brp) abundance, but no changes in postsynaptic glutamate receptors. Ultrastructural changes in muscle and NMJ development at these single muscle fibers were sufficient to lead to observable changes in neuromuscular transduction and ultimately, locomotory behavior.
GALEON: A Comprehensive Bioinformatic Tool to Analyse and Visualise Gene Clusters in Complete Genomes
Authors: Pisarenco Vadim A. , Vizueta Joel , Rozas Julio 
Published: April 2024

ABSTRACTMotivationGene clusters, defined as a set of genes encoding functionally-related proteins, are abundant in eukaryotic genomes. Despite the increasing availability of chromosome-level genomes, the comprehensive analysis of gene family evolution remains largely unexplored, particularly for large and highly dynamic gene families or those including very recent family members. These challenges stem from limitations in genome assembly contiguity, particularly in repetitive regions such as large gene clusters. Recent advancements in sequencing technology, such as long reads and chromatin contact mapping, hold promise in addressing these challenges.ResultsTo facilitate the identification, analysis, and visualisation of physically clustered gene family members within chromosome-level genomes, we introduce GALEON, a user-friendly bioinformatic tool. GALEON identifies gene clusters by studying the spatial distribution of pairwise physical distances among gene family members along with the genome-wide gene density. The pipeline also enables the simultaneous analysis and comparison of two gene families, and allows the exploration of the relationship between physical and evolutionary distances. This tool offers a novel approach for studying the origin and evolution of gene families.Availability and ImplementationGALEON is freely available fromhttp://www.ub.edu/softevol/galeon, and fromhttps://github.com/molevol-ub/galeon
Orange Maker: a CRISPR/Cas9-mediated genome editing and screening project to generate orange-eyed DarkJedi GAL4 lines by undergraduate students
Authors: Park Hee Su , Gross Anna C. , Oh Seungjae , Kim Nam Chul 
Published: April 2024

AbstractOne of the greatest strengths ofDrosophilagenetics is its easily observable and selectable phenotypic markers. The mini-white marker has been widely used as a transgenic marker for Drosophila transgenesis. Flies carrying a mini-white construct can exhibit various eye colors ranging from pale orange to intense red, depending on the insertion site and gene dosage. Because the two copies of the mini-white marker show a stronger orange color, this is often used for selecting progenies carrying two transgenes together in a single chromosome after chromosomal recombination. However, some GAL4 lines available in the fly community originally have very strong red eyes. Without employing another marker, such as GFP, generating a recombinant chromosome with the strong red-eyed GAL4 and a desired UAS-transgene construct may be difficult. Therefore, we decided to change the red eyes of GAL4 lines to orange color. To change the eye color of the fly, we tested the CRISPR/Cas9 method with a guide RNA targeting the white gene with OK371-GAL4 and elav-GAL4. After a simple screening, we have successfully obtained multiple lines of orange-eyed OK371-GAL4 and elav-GAL4 that still maintain their original expression patterns. All of these simple experiments were performed by undergraduate students, allowing them to learn about a variety of different genetic experiments and genome editing while contributing to the fly research community by creating fruit fly lines that will be used in real-world research.