bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does Everyone See the Same Thing?
Authors: Goldstein Naomi E. S. , Serico Jennifer M. , Haney-Caron Emily , Giallella Christy L. , Kalbeitzer Rachel , Zelechoski Amanda D. , Riggs Romaine Christina L. , Kemp Kathleen 
Published: February 2024

Abstract
This chapter provides the participant materials for Session 4 of the Juvenile Justice Anger Management (JJAM) Treatment for Girls. This session focuses on the ability to see things from different points of view and to think of different reasons why a person did something. Having more information about a situation should help one understand the situation better and therefore have a better reaction. When someone else is angry, it is usually because of several different reasons. It is thus important to try to think about the situation from the other person’s point of view. The participant feedback form allows participants to reflect on examples of situations where they can practice looking at things from a different perspective.
Self-Control
Authors: Goldstein Naomi E. S. , Serico Jennifer M. , Haney-Caron Emily , Giallella Christy L. , Kalbeitzer Rachel , Zelechoski Amanda D. , Riggs Romaine Christina L. , Kemp Kathleen 
Published: February 2024

Abstract
This chapter provides the participant materials for Session 7 of the Juvenile Justice Anger Management (JJAM) Treatment for Girls. This session teaches the girls to practice self-control when they are angry. It is hard to think when one is angry, but tools can help one stay calm and deal with one’s anger without getting into trouble. One tool is to take a deep breath before talking back to someone so that one can have time to think about how to respond. The participant feedback form identifies acts of social aggression and allows participants to reflect on examples of situations where they can practice self-control.
Preparing for Our Futures
Authors: Goldstein Naomi E. S. , Serico Jennifer M. , Haney-Caron Emily , Giallella Christy L. , Kalbeitzer Rachel , Zelechoski Amanda D. , Riggs Romaine Christina L. , Kemp Kathleen 
Published: February 2024

Abstract
This chapter provides the participant materials for Session 14 of the Juvenile Justice Anger Management (JJAM) Treatment for Girls. In this session the girls learn how to prepare plans for the future. This includes the process of figuring out how to tell important people about the anger management tools they learned and how to ask for help. Planning ahead means thinking about one’s goals and writing them down. An example of a goal is to get better grades in school by the end of the year. When a participant is angry and needs help remembering these tools, it is useful for her to talk to her building block support people.
Digital Microscopy Augmented by Artificial Intelligence to Interpret Bone Marrow Samples for Hematological Diseases
Authors: Bermejo-Peláez David , Rueda Charro Sandra , García Roa María , Trelles-Martínez Roberto , Bobes-Fernández Alejandro , Hidalgo Soto Marta , García-Vicente Roberto , Morales María Luz , Rodríguez-García Alba , Ortiz-Ruiz Alejandra , Blanco Sánchez Alberto , Mousa Urbina Adriana , Álamo Elisa , Lin Lin , Dacal Elena , Cuadrado Daniel , Postigo María , Vladimirov Alexander , Garcia-Villena Jaime , Santos Andrés , Ledesma-Carbayo María Jesús , Ayala Rosa , Martínez-López Joaquín , Linares María , Luengo-Oroz Miguel 
Published: February 2024

Abstract
Analysis of bone marrow aspirates (BMAs) is an essential step in the diagnosis of hematological disorders. This analysis is usually performed based on a visual examination of samples under a conventional optical microscope, which involves a labor-intensive process, limited by clinical experience and subject to high observer variability. In this work, we present a comprehensive digital microscopy system that enables BMA analysis for cell type counting and differentiation in an efficient and objective manner. This system not only provides an accessible and simple method to digitize, store, and analyze BMA samples remotely but is also supported by an Artificial Intelligence (AI) pipeline that accelerates the differential cell counting process and reduces interobserver variability. It has been designed to integrate AI algorithms with the daily clinical routine and can be used in any regular hospital workflow.
Accurate Fourier-space statistics for line intensity mapping: Cartesian grid sampling without aliased power
Authors: Cunnington Steven , Wolz Laura 
Published: February 2024

ABSTRACT
Estimators for n-point clustering statistics in Fourier-space demand that modern surveys of large-scale structure be transformed to Cartesian coordinates to perform Fast Fourier Transforms (FFTs). In this work, we explore this transformation in the context of pixelized line intensity maps (LIM), highlighting potential biasing effects on power-spectrum measurements. Current analyses often avoid a complete resampling of the data by approximating survey geometry as rectangular in Cartesian space, an increasingly inaccurate assumption for modern wide-sky surveys. Our simulations of a $20\, {\times }\, 20\, \text{deg}^2$ 21 cm LIM survey at $0.34\, {\lt }\, z\, {\lt }\, 0.54$ show this assumption biases power-spectrum measurements by ${\gt }\, 20~{{\ \rm per\ cent}}$ across all scales. We therefore present a more robust framework for regridding the voxel intensities on to a 3D FFT field by coordinate transforming large numbers of Monte-Carlo sampling particles. Whilst this unbiases power-spectrum measurements on large scales, smaller scale discrepancies remain, caused by structure smoothing and aliasing from separations unresolved by the grid. To correct these effects, we introduce modelling techniques, higher order particle assignments, and interlaced FFT grids to suppress the aliased power. Using a piecewise cubic spline (PCS) particle assignment and an interlaced FFT field, we achieve sub-per cent accuracy up to 80 per cent of the Nyquist frequency for our 21 cm LIM simulations. We find a more subtle hierarchical improvement in results for higher order assignment schemes, relative to the gains made for galaxy surveys, which we attribute to the extra complexity in LIM from additional discretizing steps. python code accompanying this paper is available at github.com/stevecunnington/gridimp.
Rapid neutron star cooling triggered by dark matter
Authors: Ávila Afonso , Giangrandi Edoardo , Sagun Violetta , Ivanytskyi Oleksii , Providência Constança 
Published: February 2024

ABSTRACT
We study the effect of asymmetric fermionic dark matter (DM) on the thermal evolution of neutron stars (NSs). No interaction between DM and baryonic matter is assumed, except the gravitational one. Using the two-fluid formalism, we show that DM accumulated in the core of a star pulls inwards the outer baryonic layers of the star, increasing the baryonic density in the NS core. As a result, it significantly affects the star’s thermal evolution by triggering an early onset of the direct Urca (DU) process and modifying the photon emission from the surface caused by the decrease of the radius. Thus, due to the gravitational pull of DM, the DU process becomes kinematically allowed for stars with lower masses. Based on these results, we discuss the importance of NS observations at different distances from the Galactic Centre. Since the DM distribution peaks towards the Galactic Centre, NSs in this region are expected to contain higher DM fractions that could lead to a different cooling behavior.
Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analyses
Authors: Campos Leonardo R S , Trefflich Sheyla , Morais Diego A A , Imparato Danilo O , Chagas Vinicius S , Albanus Ricardo D’Oliveira , Dalmolin Rodrigo J S , Castro Mauro A A 
Published: February 2024

Abstract
Orthology information has been used for searching patterns in high-dimensional data, allowing transferring functional information between species. The key concept behind this strategy is that orthologous genes share ancestry to some extent. While reconstructing the history of a single gene is feasible with the existing computational resources, the reconstruction of entire biological systems remains challenging. In this study, we present Bridge, a new algorithm designed to infer the evolutionary root of orthologous genes in large-scale evolutionary analyses. The Bridge algorithm infers the evolutionary root of a given gene based on the distribution of its orthologs in a species tree. The Bridge algorithm is implemented in R and can be used either to assess genetic changes across the evolutionary history of orthologous groups or to infer the onset of specific traits in a biological system.
The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics
Authors: Garcia Sònia , Kovarik Ales , Maiwald Sophie , Mann Ludwig , Schmidt Nicola , Pascual-Díaz Joan Pere , Vitales Daniel , Weber Beatrice , Heitkam Tony 
Published: February 2024

Abstract
Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements are genetic elements with not much in common: whereas ribosomal DNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, transposable elements are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (ribosomal DNAs) versus organization in a dispersed manner (transposable elements); evolution in a concerted manner (ribosomal DNAs) versus evolution by diversification (transposable elements); and activity that prolongs genomic stability (ribosomal DNAs) versus activity that shortens it (transposable elements). Re-visiting relevant instances in which ribosomal DNA–transposable element interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales, (2) they exchange structural motifs and can enter co-evolution processes, (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging, and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional, and evolutionary characteristics of both ribosomal DNAs and transposable elements, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding ribosomal DNA–transposable element associations.
A multi-institutional phase I study of acetazolamide with temozolomide in adults with newly diagnosed MGMT-methylated malignant glioma
Authors: Driscoll Riley K , Lyne Sean B , Voce David J , Maraka Stefania , Gondi Vinai , Chmura Steven J , Dixit Karan S , Kumthekar Priya U , Karrison Theodore G , Pytel Peter , Collins John M , Stupp Roger , Merrell Ryan T , Lukas Rimas V , Yamini Bakhtiar 
Published: February 2024

Abstract

Background
A significant unmet need exists for the treatment of glioblastoma, IDH-wildtype (GBM). Preclinical work shows that acetazolamide sensitizes GBM to temozolomide (TMZ) by overcoming TMZ resistance due to BCL-3-dependent upregulation of carbonic anhydrase. Acetazolamide is Food and Drug Administration-approved for the treatment of altitude sickness. Drug repurposing enables the application of drugs to diseases beyond initial indications. This multi-institutional, open-label, phase I trial examined a combination of acetazolamide and TMZ in patients with MGMT promoter-methylated high-grade glioma.

Methods
A total of 24 patients (GBM, IDH-wildtype = 22; Grade 4 astrocytoma, IDH-mutant = 1; Grade 3 astrocytoma, IDH-mutant = 1) were accrued over 17 months. All patients received oral acetazolamide (250 mg BID for 7 days increased to 500 mg BID for Days 8–21 of each 28-day cycle) during the adjuvant phase of TMZ for up to 6 cycles.

Results
No patient had a dose-limiting toxicity. Adverse events were consistent with known sequelae of acetazolamide and TMZ. In the 23 WHO Grade 4 patients, the median overall survival (OS) was 30.1 months and the median progression-free survival was 16.0 months. The 2-year OS was 60.9%. In total 37% of the study population had high BCL-3 staining and trended toward shorter OS (17.2 months vs N.R., P = .06).

Conclusions
The addition of acetazolamide is safe and tolerable in GBM patients receiving standard TMZ. Survival results compare favorably to historical data from randomized trials in patients with MGMT promoter-methylated GBM and support examination of acetazolamide in a randomized trial. BCL-3 expression is a potential biomarker for prognosis in GBM or for patients more likely to benefit from TMZ.
Diagnostic Accuracy of Point-of-Care Gram Stains in Obstructive Pyelonephritis due to Ureteral Stones
Authors: Hayano Satoshi , Hidaka Toshiya , Tadakuma Risako , Kashima Masayuki 
Published: February 2024

Abstract

Background
The diagnostic utility of point-of-care (POC) Gram stains for obstructive pyelonephritis with hydronephrosis is not well established. The current study aimed to assess the diagnostic accuracy of urine Gram stains in patients with obstructive pyelonephritis due to ureteral stones.

Methods
A retrospective observational study was conducted on patients with obstructive pyelonephritis admitted to our hospital between January 2011 and December 2021. The diagnostic accuracy of Gram stains was evaluated based on the severity of hydronephrosis, including Gram stains performed by both trained physicians and microbiological technicians.

Results
After analyzing 210 patients, POC Gram stains of bladder urine presented a sensitivity, specificity, positive predictive value, and negative predictive value of 86.8%, 81.8%, 93.7%, and 66.7%, respectively, for gram-negative rods and 65.7%, 83.4%, 48.9%, and 91.0%, respectively, for gram-positive cocci. The agreement between POC Gram stains and urine culture was good for gram-negative rods, with a kappa (κ) coefficient of 0.637 and agreement rate of 85.6%, and moderate for gram-positive cocci, with a κ coefficient of 0.435 and agreement rate of 80%. The agreement between POC Gram stains and bladder urine culture results for gram-negative rods was higher in the mild hydronephrosis group (κ coefficient = 0.677) than in the severe hydronephrosis group (κ coefficient = 0.466). Discrepancies in Gram stain results between physicians and technicians were observed in 21 of 180 cases (11.7%).

Conclusions
POC Gram stains for gram-negative rods may be a useful diagnostic tool for obstructive pyelonephritis, particularly in cases of mild hydronephrosis.
Divergent Protein Redox Dynamics and Their Relationship with Electron Transport Efficiency during Photosynthesis Induction
Authors: Yoshida Keisuke , Hisabori Toru 
Published: February 2024

AbstractVarious chloroplast proteins are activated/deactivated during the light/dark cycle via the redox regulation system. Although the photosynthetic electron transport chain provides reducing power to redox-sensitive proteins via the ferredoxin (Fd)/thioredoxin (Trx) pathway for their enzymatic activity control, how the redox states of individual proteins are linked to electron transport efficiency remains uncharacterized. Here we addressed this subject with a focus on the photosynthetic induction phase. We used Arabidopsis plants, in which the amount of Fd–Trx reductase (FTR), a core component in the Fd/Trx pathway, was genetically altered. Several chloroplast proteins showed different redox shift responses toward low- and high-light treatments. The light-dependent reduction of Calvin–Benson cycle enzymes fructose 1,6-bisphosphatase (FBPase) and sedoheptulose 1,7-bisphosphatase (SBPase) was partially impaired in the FTR-knockdown ftrb mutant. Simultaneous analyses of chlorophyll fluorescence and P700 absorbance change indicated that the induction of the electron transport reactions was delayed in the ftrb mutant. FTR overexpression also mildly affected the reduction patterns of FBPase and SBPase under high-light conditions, which were accompanied by the modification of electron transport properties. Accordingly, the redox states of FBPase and SBPase were linearly correlated with electron transport rates. In contrast, ATP synthase was highly reduced even when electron transport reactions were not fully induced. Furthermore, the redox response of proton gradient regulation 5-like photosynthetic phenotype1 (PGRL1; a protein involved in cyclic electron transport) did not correlate with electron transport rates. Our results provide insights into the working dynamics of the redox regulation system and their differential associations with photosynthetic electron transport efficiency.
Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations
Authors: Torralba Babil , Blanc Stéphane , Michalakis Yannis 
Published: February 2024

Abstract
Single-stranded DNA multipartite viruses, which mostly consist of members of the genus Begomovirus, family Geminiviridae, and all members of the family Nanoviridae, partly resolve the cost of genomic integrity maintenance through two remarkable capacities. They are able to systemically infect a host even when their genomic segments are not together in the same host cell, and these segments can be separately transmitted by insect vectors from host to host. These capacities potentially allow such viruses to reassort at a much larger spatial scale, since reassortants could arise from parental genotypes that do not co-infect the same cell or even the same host. To assess the limitations affecting reassortment and their implications in genome integrity maintenance, the objective of this review is to identify putative molecular constraints influencing reassorted segments throughout the infection cycle and to confront expectations based on these constraints with empirical observations. Trans-replication of the reassorted segments emerges as the major constraint, while encapsidation, viral movement, and transmission compatibilities appear more permissive. Confronting the available molecular data and the resulting predictions on reassortments to field population surveys reveals notable discrepancies, particularly a surprising rarity of interspecific natural reassortments within the Nanoviridae family. These apparent discrepancies unveil important knowledge gaps in the biology of ssDNA multipartite viruses and call for further investigation on the role of reassortment in their biology.
Chromosome-Scale Genome Sequence of Nothopassalora personata (syn. Cercosporidium personatum), a Devastating Fungal Pathogen of Peanut
Authors: Gonzales Maricel , Abernathy Brian L. , Kemerait Robert , Bertioli David , Brewer Marin , Bertioli Soraya 
Published: February 2024

Nothopassalora personata, the causal agent of late leaf spot, is an economically important fungus that poses a significant threat to peanut production worldwide. Currently, studies on N. personata are focused on epidemiology, host resistance, early environmental detection, and molecular studies based on a limited number of genes for classification. A high-quality whole-genome sequence can be a valuable tool for studying complex species and identifying molecular mechanisms in pathogenicity and adaptation. This study reports a high-quality, chromosome-scale genome assembly for N. personata with a total length of 54.6 Mb, an N50 of 2.54 Mb, a longest contig length of 4.47 Mb, and a BUSCO genome completeness score of 99.5% with mostly single-copy genes. Genome annotation revealed 11,295 protein-encoding genes and 12,121 transcripts in which 411 of the 995 predicted proteins were putative effectors. Genome comparison with the closely related fungi Dothistroma septosporum NZE10 and Fulvia fulva (syn . Passalora fulva, Cladosporium fulvum) isolate Race 5 revealed 13 chromosomes. This genome sequence resource can be used as a reference for aligning sequences of multiple isolates to provide relevant information on the diversity and population genetic structure of N. personata to further inform peanut resistance breeding programs and devise the best disease management strategies. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Prospectively Collected Comparison of Outcomes Between Surgically and Conservatively Treated Patients With Adolescent Idiopathic Scoliosis
Authors: Whitaker Colin M. , Miyanji Firoz , Samdani Amer F. , Pahys Joshua M. , Sponseller Paul D. , Bryan Tracey P. , Newton Peter O. ,   Harms Study Group, Hwang Steven W. 
Published: February 2024

Study Design.
Retrospective review of a prospectively collected multicenter registry.

Objective.
To evaluate health-related quality of life (HRQOL) measures in an operative cohort of patients (OP) and compare them with a matched nonoperative cohort (NON).

Summary of Background Data.
Historically, the surgical outcomes of adolescent idiopathic scoliosis (AIS) have been radiographically evaluated. However, the importance of HRQOL measures and their impact on surgical outcomes are increasingly being understood.

Materials and Methods.
We identified 90 NON patients with curves in the operative range who were observed for at least two years. These patients were matched with an OP cohort of 689 patients. All patients completed the Scoliosis Research Society-22 (SRS-22) questionnaire at the initial evaluation and at a minimum of two-year follow-up. Subgroup comparisons were based on curve type: primary thoracic (Th), primary thoracolumbar/lumbar (TL/L), and double major (DM) curves.

Results.
The preoperative major curves in the Th, TL/L, and DM OP subgroups averaged 50.4°, 45.4°, and 51.5°, respectively, and 49.4°, 43.7°, and 48.9° in the NON cohort (P>0.05). At two years postoperatively, the major curve in the Th, TL/L, and DM OP subgroups improved to 19.0°, 19.2°, and 19.3°, respectively, compared with the progression to 51.3°, 44.5°, and 49.7° in the NON group at two-year follow-up (P<0.05). The SRS-22 self-image, mental health, satisfaction, and total scores at the two-year follow-up were significantly better in all OP subgroups (P<0.001) but remained largely unchanged in the NON group. A significant percentage of patients (P<0.001) in the OP cohort reported better SRS-22 scores at the two-year follow-up in the self-image, mental health, and satisfaction domains than the NON group at two years.

Conclusions.
Surgically treated patients with AIS have improved HRQOL outcomes in several domains compared with age-matched and curve magnitude-matched nonoperatively treated patients at two-year follow-up.