bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing reagents and techniques for identifying RhCE variants in routine serological testing
Authors: de Paula Vendrame Tatiane Aparecida , Arnoni Carine Prisco , Devides Giovana Faria , Silva Nayara Moraes , Cortez Afonso José Pereira , Roche Moreira Latini Flavia , Castilho Lilian 
Published: January 2025

AbstractBackground and ObjectivesIdentifying RhCE variants is essential to prevent alloimmunization and manage complex cases. Unfortunately, these variants are often only detected after antibody formation, as they may go unnoticed in serological tests. This study aimed to assess monoclonal antisera using various methodologies to define the reactivity patterns of some variants by variable expression of RhCE antigens.Materials and MethodsSamples were chosen based on atypical reactivity on routine RhCE typing of donors, screening of Afro‐descendant donors using tube testing and patient samples with antibodies against their own antigens. All 53 samples were tested using tube, gel and microplate tests with five antisera. Antigen expression was assessed by flow cytometry, and RhCE variants were molecularly classified.ResultsTube test screening of African descent donors proved more effective in identifying a broad range of weak or partial antigens, particularly when using anti‐e composed of MS‐21, MS‐16, MS63 clones and anti‐c from the MS8011531019 clone. Automated instrument phenotyping successfully identified samples with RHCE*ceJAL allele, while most other variants were detected as positive (4+), similar to gel test, which intensified most reactions. When comparing methods and antisera for detecting variant e antigens, tube test identified a higher percentage of weak samples (63%–77%) compared with microplate (35%) and gel tests (14%).ConclusionThe results highlight the critical role of tube test in serological routines and the need to select clones capable of identifying RhCE variants. Detecting reduced RhCE antigen expression during routine serological testing can guide further molecular investigations and help prevent Rh alloimmunization.
Effect of Paternity Leave or Fathers’ Parental Leave on Infant Health: a Systematic Review Protocol
Authors: Nick Jan M. , Sahin Safiye , Roberts Lisa R. , Hatton Adorée , Cafferky Bryan 
Published: January 2025

Objective:
The objective of the systematic review will be to evaluate the effect of paternity leave or fathers’ parental leave on infant mortality rate, hospitalization, vaccination compliance, and breastfeeding duration.

Introduction:
Current studies indicate that paternity leave positively affects infant health, but there is a significant lack of synthesized research on its impact on key infant health indicators. A systematic review of the existing evidence will help identify best practices and guide further research and policy development in this area.

Inclusion criteria:
The proposed systematic review will include studies such as experimental, quasi-experimental, and analytic observational studies, conducted among infants less than 1 year of age, exploring the effect of fathers’ paternity leave or fathers’ parental leave on the identified infant health outcomes.

Methods:
The review will follow the JBI methodology for systematic reviews of effectiveness. A 3-step search strategy will be used, with no date or language restrictions. Study selection will also follow a 3-step process, including critical appraisal to determine methodological quality. Each step will be conducted by 2 independent reviewers; disagreements will be resolved through discussion or with other team members. The team will extract data using standardized templates from JBI SUMARI, then synthesize and conduct meta-analysis, if possible. If not, narrative synthesis will be conducted. Finally, the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach to determine certainty of evidence will be used to create a summary of findings.

Review registration number:
This protocol has been registered in PROSPERO: CRD42024502533.
Overheard at a conference: an in-class activity to foster classroom discussion on ethics and experimental systems in microbiology research
Authors: Tremblay Yannick D. N. , Thomassin Jenny-Lee 
Published: January 2025

ABSTRACT

Responsible conduct of research and ethics are key components of microbiology and are carefully considered at all steps from project conception, design, data analysis to publication, and post-publication use of samples. Yet stand-alone courses covering these topics are not always core components of undergraduate biomedical education curricula. Here, we describe a classroom activity for undergraduate students designed to promote increased understanding of ethics and experimental design in biomedical research.
Peeling Close to the Orientability Threshold – Spatial Coupling in Hashing-Based Data Structures
Authors: Walzer Stefan 
Published: January 2025

In multiple-choice data structures each element

\(x\)

in a set

\(S\)

of

\(m\)

keys
is associated with a random set
e(x)
⊆ [
n
] of
buckets
with capacity

\(\ell \ge 1\)

by hash functions. This setting is captured by the hypergraph

\(H=([n],\{e(x)\mid x \in S\})\)

. Accomodating each key in an associated bucket amounts to finding an
ℓ-orientation
of

\(H\)

assigning to each hyperedge an incident vertex such that each vertex is assigned at most ℓ hyperedges. If each subhypergraph of

\(H\)

has minimum degree at most ℓ, then an ℓ-orientation can be found greedily and

\(H\)

is called
ℓ-peelable
. Peelability has a central role in invertible Bloom lookup tables and can speed up the construction of retrieval data structures, perfect hash functions and cuckoo hash tables.

Many hypergraphs exhibit sharp density thresholds with respect to ℓ-orientability and ℓ-peelability, i.e. as the density

\(c=\frac{m}{n}\)

grows past a critical value, the probability of these properties drops from almost

\(1\)

to almost

\(0\)

. In fully random

\(k\)

-uniform hypergraphs the thresholds

\(c_{k,l}^\ast\)

for ℓ-orientability significantly exceed the thresholds for ℓ-peelability. In this paper, for every

\(k \ge 2\)

and

\(\ell \ge 1\)

with

\((k,\ell)\ne(2,1)\)

and every

\(z>0\)

, we construct a new family of random

\(k\)

-uniform hypergraphs with i.i.d. random hyperedges such that
both
the ℓ-peelability and the ℓ-orientability thresholds approach

\(c_{k,l}^\ast\)

as

\(z \rightarrow \infty\)

. In particular we achieve

\(1\)

-peelability at densities arbitrarily close to

\(1\)

, extending the reach of greedy algorithms.

Our construction is simple: The

\(n\)

vertices are linearly ordered and each hyperedge selects its

\(k\)

elements uniformly at random from a random range of

\(\frac{n}{z+1}\)

consecutive vertices. We thus exploit the phenomenon of
threshold saturation
via
spatial coupling
discovered in the context of low-density parity-check codes. Once the connection to data structures is in plain sight, a framework by Kudekar, Kudekar, Richardson and Urbanke [42] does the heavy lifting in our proof.

We demonstrate the usefulness of our construction using our hypergraphs as a drop-in replacement in a retrieval data structure by Botelho et al. [9]. This reduces memory usage from

\(\approx1.23m\)

bits to

\(\approx1.12m\)

bits (for input size

\(m\)

). Using

\(k>3\)

attains, at small sacrifices in running time, further improvements to memory usage.
Understanding and Preventing Advanced Gastric Cancer in Young Hispanic Patients
Authors: Buxbaum James L. 
Published: January 2025

Abstract
The risk of gastric cancer among immigrants from countries where Helicobacter pylori is endemic greatly exceeds those born in the United States. Among patients in the Los Angeles safety-net health system, the risk of advanced and fatal gastric cancer is higher in Hispanic versus non-Hispanic patients. There is an urgent need to define whether this reflects concomitant illnesses, such as metabolic disease, occupational exposures, or differential access to H. pylori eradication and endoscopic gastric cancer screening programs.
See related article by Klingbeil et al., p. 75
Examining Lung Cancer Screening Uptake in the United States: Recent Research and Limitations of Public-Use Data
Authors: Maki Kristin G. , Tan Naomi Q.P. , Volk Robert J. , Toumazis Iakovos 
Published: January 2025

Abstract
Eligibility criteria for lung cancer screening (LCS) were updated by the Centers for Medicare & Medicaid Services in 2022 following an updated recommendation from the United States Preventive Services Task Force. Recently, research has examined LCS use in the United States following this change, which centered on lowering the age to begin screening from 55 to 50 years and the smoking history threshold from 30 to 20 pack-years. These studies, including the accompanying article from Gudina and colleagues, have used the 2022 Behavioral Risk Factors Surveillance System data, which are publicly available and nationally representative. Although increases in LCS use have been reported in all studies, screening remains low compared with other population-level cancer screening programs, highlighting the need for interventions to improve LCS uptake and adherence. Data limitations from population-based surveys may affect the ability to accuracy track LCS rates. Additional, high-quality data are needed to further assess the uptake of—and adherence to—LCS following the updated eligibility criteria.
See related article by Gudina et al., p. 35
Host tissue factors predict immune surveillance and therapeutic outcomes in gastric cancer
Authors: Abate Miseker , Stroobant Emily , Fei Teng , Lin Ya-Hui , Shimada Shoji , Drebin Harrison , Chen Eunise , Tang Laura H. , Shah Sohrab P. , Wolchok Jedd D. , Janjigian Yelena Y. , Strong Vivian E. , Vardhana Santosha A. 
Published: January 2025

Abstract
The immune composition of solid tumors is typically inferred from biomarkers, such as histologic and molecular classifications, somatic mutational burden, and PD-L1 expression. However, the extent to which these biomarkers predict the immune landscape in gastric adenocarcinoma—an aggressive cancer often linked to chronic inflammation—remains poorly understood. We leveraged high-dimensional spectral cytometry to generate a comprehensive single-cell immune landscape of tumors, normal tissue, and lymph nodes from patients in the Western Hemisphere with gastric adenocarcinoma. The immune composition of gastric tumors could not be predicted by traditional metrics such as tumor histology, molecular classification, mutational burden, or PD-L1 expression via IHC. Instead, our findings revealed that innate immune surveillance within tumors could be anticipated by the immune profile of the normal gastric mucosa. Additionally, distinct T-cell states in the lymph nodes were linked to the accumulation of activated and memory-like CD8+ tumor-infiltrating lymphocytes (TILs). Unbiased re-classification of patients based on tumor-specific immune infiltrate generated four distinct subtypes with varying immune compositions. Tumors with a T-cell-dominant immune subtype, which spanned TCGA molecular subtypes, were exclusively associated with superior responses to immunotherapy. Parallel analysis of metastatic gastric cancer patients treated with immune checkpoint blockade showed that patients who responded to immunotherapy had a pre-treatment tumor composition that corresponded to a T-cell-dominant immune subtype from our analysis. Taken together, this work identifies key host-specific factors associated with intratumoral immune composition in gastric cancer and offers an immunological classification system that can effectively identify patients likely to benefit from immune-based therapies.
Painting Humanitarian Experiences at Sea: The Raft of the Medusa
Authors: Martín-Moruno Dolores 
Published: January 2025

Abstract
Taking We’re Not All in the Same Boat (2015) – Banksy’s reinterpretation of Théodore Géricault’s The Raft of the Medusa (1819) – as its departure point, this article explores the maritime routes through which artists have produced and circulated humanitarian experiences amongst international audiences as a colourful palette of embodied practices, emotions, sensations, feelings, perceptions and thoughts. Drawing on the accounts of the Medusa’s survivors, I analyse the advocacy strategies used by Géricault in his painting to make the spectator feel the sufferings experienced by the shipwrecked aboard the raft through the hallucinations provoked by calenture: a madness which affected sailors who crossed the tropics. Ultimately, a comparison between Géricault’s and Banksy’s artworks allows us to sail on a raft – the humanitarian theatre par excellence at sea – to connect past and present-day migratory journeys through the legacies of colonialism and denounce Western immigration controls by performing solidarity towards refugees.
Automated quantification of anterior chamber cells using swept-source anterior segment optical coherence tomography
Authors: Pillar Shani , Kadomoto Shin , Chen Keren , Gonzalez Saitiel Sandoval , Cherian Nina , Privratsky Joseph K. , Zargari Nicolette , Jackson Nicholas J. , Corradetti Giulia , Chen Judy L. , Sadda SriniVas R. , Holland Gary N. , Tsui Edmund 
Published: January 2025

Abstract
Purpose
To validate automated counts of presumed anterior chamber (AC) cells in eyes with histories of uveitis involving the anterior segment using swept-source (SS) anterior segment optical coherence tomography (AS-OCT) against manual counts and compare automated counts against Standardized Uveitis Nomenclature (SUN) criteria.

Methods
Eyes were imaged with the ANTERION SS AS-OCT device (Heidelberg Engineering). A fully automated custom algorithm quantified the number of hyper-reflective foci (HRF) in line-scan images. Automated and manual counts were compared using interclass correlation (ICC) and Pearson correlation coefficient. Automated counts were compared to SUN grades using a mixed-effects linear regression model.

Results
90 eyes (54 participants) were included; 67 eyes (41 participants) had histories of uveitis, while 23 eyes (13 healthy participants) served as controls. ICC comparing automated to manual counts was 0.99 and the Pearson correlation coefficient was 0.98. Eyes at each SUN grade with corresponding median HRF (interquartile range [IQR]) were: Grade 0, 42 eyes, 2 HRF (0,4); 0.5+, 10 eyes, 10 HRF (8,15); 1+, 9 eyes, 22 HRF (15,33); 2+, 3 eyes, 27 HRF; 3+, 2 eyes, 128 HRF; 4+, 1 eye, 474 HRF. For every 1-step increase in grade, automated count increased by 38 (p < 0.001) or 293% (Pearson correlation coefficient 0.80, p < 0.001). Automated counts differed significantly between clinically inactive eyes (2 HRF [0,4]) and controls (0 HRF [0,1], p = 0.02).

Conclusions
Our algorithm accurately counts HRF when compared to manual counts, with strong correlation to SUN clinical grades. SS AS-OCT offers the advantage of imaging of the entire AC and may allow detection of subclinical inflammation in eyes that appear clinically inactive.
Measuring fluid balance in end-stage renal disease with a wearable bioimpedance sensor
Authors: Bremnes Frida , Øien Cecilia Montgomery , Kvaerness Jørn , Jaatun Ellen Andreassen , Aas Sigve Nyvik , Saether Terje , Lund Henrik , Romundstad Solfrid 
Published: January 2025

Abstract
Background
Accurate assessment of fluid volume and hydration status is essential in many disease states, including patients with chronic kidney disease. The aim of this study was to investigate the ability of a wearable continuous bioimpedance sensor to detect changes in fluid volume in patients undergoing regular hemodialysis (HD).

Methods
31 patients with end-stage renal disease were enrolled and monitored with a sensor patch (Re:Balans®) on the upper back through two consecutive HD sessions and the interdialytic period between. The extracellular resistance RE was calculated from multi-frequency bioimpedance measurements and was hypothesized to correlate with the amount of extracted fluid during dialysis.

Results
Only HD sessions with a positive net fluid extraction were included in the primary analysis. Participants had an increase of 7.5 ± 4.3 Ω (Ohm) in RE during the first HD and 6.2 ± 2.3 Ω during the second HD, and a fluid extraction (ultrafiltration (UF) volume) of 1.5 ± 0.8 L and 1.2 ± 0.6 L, respectively. The relative change in RE during HD correlated strongly with UF volume (r = 0.82, p < 0.001). During the interdialytic period, the patients had a mean decrease in RE of 6.0 ± 3.5 Ω. Longitudinal changes in RE (%) and body weight (kg) over the entire study period was negatively correlated (r = -0.61 p < 0.001). Longitudinal changes in blood samples and cardiovascular changes were also in agreement with changes in weight and RE.

Conclusions
The results of this clinical investigation indicate that the investigational device is capable of tracking both rapid and gradual changes in hydration status in patients undergoing regular HD.
COVID-19 workplace countermeasures that occupational physicians could not change in Japan: a qualitative study
Authors: Igarashi Yu , Tateishi Seiichiro , Matsuoka Juri , Sawajima Tomoko , Kawasumi Mika , Harada Arisa , Mori Koji 
Published: January 2025

Abstract
Background
During the COVID-19 pandemic, information and circumstances changed from moment to moment, including the accumulation of scientific knowledge, the emergence of variants, social tolerance, and government policy. Therefore, it was important to adapt workplace countermeasures punctually and flexibly based on scientific evidence and according to circumstances. However, there has been no assessment of changes in workplace countermeasures. With a view toward preparedness for future pandemics, we surveyed COVID-19 workplace countermeasures that occupational physicians considered as needing to be changed but went unchanged.

Methods
We invited 685 professional occupational physicians certified by Japan Society for Occupational Health to complete an online questionnaire by sending postcards with QR codes. The main questions concerned countermeasures that the participants wanted to change but could not. The survey period was from February 21 to April 28, 2022. The responses were analyzed using the KJ method.

Results
Of the 168 invitees (24.5%) who responded to the survey, 125 reported countermeasures that needed to be changed (total count: 254). The responses were categorized into basic systems, occupational health services, workplace countermeasures, vaccines, and incidents, with a code count of 7, 8,147, 10, and 82, respectively. The type of countermeasure was 115 for countermeasures to be strengthened (CBS), 110 for measures to be mitigated (CBM), and 29 for neither.

Conclusions
Often-mentioned CBS were increased teleworking, strengthened ventilation, smoking cessation, and promotion of vaccines. Often-mentioned CBM were relaxation of protective equipment rules, discontinued environmental disinfection, and shorted isolation and reinstatement. In the early pandemic phases, CBSs were frequently mentioned, whereas CBMs were featured more prominently in the latter phases. The survey revealed countermeasures that occupational physicians thought needed to be changed but were not changed in practice. For future responses to emerging and reemerging infectious diseases, it will be necessary to establish rules compatible with flexible modification of workplace countermeasures in response to changing circumstances.
Changes to muscle and fascia tissue after eighteen days of ankle immobilization post-ankle sprain injury: an MRI case study
Authors: Perera Meeghage Randika , Su Pan , Holdsworth Samantha , Handsfield Geoffrey 
Published: January 2025

Abstract
Background
Ankle sprains often result in muscle atrophy and reduced range of motion, which can cause long-term ankle instabilities. Understanding the changes to muscle—such as atrophy—and concomitant changes to deep fascia—which may thicken alongside muscle loss—after ankle sprain injury is important to understanding structural changes about the joint and how they might contribute to longer-term impairments. Here, we employ advanced MRI to investigate skeletal muscle and fascial structural changes during the recovery period of one patient undergoing immobilization after ankle sprains.

Material and methods
In this case study, a participant who suffered an ankle sprain underwent initial MRI scans and, after 21 days (18 of which included immobilization), a follow-up MRI. Techniques used included proton density, 3D stack of spirals, and diffusion tensor imaging to analyse muscle and fascia changes pre- and post-injury.

Results
Results showed muscle atrophy in most shank muscles, with volume loss ranging from no change in the lateral gastrocnemius to 12.11% in the popliteus. Thigh muscles displayed hypertrophy of 6% in the hamstrings, while the quadriceps atrophied by 2.5%. Additionally, fascia thickness increased from 0.94 mm to 1.03 mm. Diffusion tensor imaging indicated that the biceps femoris experienced the most significant changes in physiological cross-sectional area, while the rectus femoris showed minimal change.

Conclusion
The findings highlight the variable responses of muscles and a notable thickening of deep fascia post-injury, underscoring its role in recovery from ankle sprains.
Enhanced recovery after surgery protocol optimizes results and cost of laparoscopic radical nephroureterectomy
Authors: Shi Jiageng , Chen Siming , Nie Jiawei , Xiong Kangping , Wang Gang , Qian Kaiyu , Zheng Hang , Wang Xinghuan 
Published: January 2025

Abstract
Purpose
To evaluate the efficacy of an enhanced recovery after surgery (ERAS) strategy for upper tract urothelial carcinoma (UTUC) patients undergoing laparoscopic radical nephroureterectomy (LRNU).

Methods
90 patients who received LRNU at Zhongnan Hospital of Wuhan University between January 2018 and July 2022 were retrospectively analyzed, including 43 in the ERAS group and 47 in the pre-ERAS group. The clinical features, postoperative complications, length of hospital stay (LOS), and hospital expenditures of the two groups were compared via t-test, Mann-Whitney test, and Chi-square test.

Results
In comparison to the pre-ERAS group, the total and postoperative LOS were significantly shorter in the ERAS group [total LOS: 15.0 (13.0–20.0) vs. 21.0 (16.0–26.0), p < 0.001; postoperative LOS: 8.0 (7.0–9.0) vs. 11.0 (9.0–13.0), p < 0.001]. The ERAS group had lower hospitalization costs than that in the pre-ERAS group [56896.40 (48324.30-67498.01) vs. 64249.83 (55574.36-81581.82), p = 0.010]. Additionally, the ERAS group experienced a reduction in postoperative fever incidence (23.4% vs. 4.7%, p = 0.011).

Conclusions
In the realm of LRNU, ERAS protocols are safe and practical for minimizing the LOS while accelerating the rehabilitation of patients undergoing LRNU. This study offers insights for enhancing ERAS protocols for UTUC patients even further.