bluuebunny/crossref_metadata_2025_split huggingface dataset:
She Asked for It? Descriptions of Victims' Behaviors Are Associated With Sentencing in Norwegian Rape Trials
Authors: Rinde Kirsten Rønning , Vučić Tea , Andresen Maria Grønland , Havnen Audun , Solem Stian 
Published: December 2024

ABSTRACTFeminist theorists have long argued that rape myths contribute to normalizing sexual assault, through belittling and denying rape victims' claims. This study examines whether descriptions of victims' behaviors are associated with sentencing in rape trials. A total of 2054 Norwegian court decisions from 2013 to 2023 in judicial records were screened. Fifty‐one of these included descriptions of the victims' behavior as operationalized by a subscale of the Illinois Rape Myth Acceptance Scale called “She Asked For It” (IRMAS‐SAFI; type of clothing, going to a room alone with a guy at a party, previous sexual behavior, saying no unclearly, and kissing). Matching cases without such descriptions were then selected, resulting in a total sample of 102 court decisions. In addition, a randomly selected comparison group (n = 51) was included for robustness analysis. Results revealed that defendants who had attacked a victim in the IRMAS‐SAFI group were sentenced to fewer months in prison (M = 25.3, SD = 20.9) than defendants from the comparison group (M = 41.7, SD = 13.3). This type of description of victims' behavior was significantly associated with shorter prison sentences when controlling for medical evidence, age of the defendant, and use of violence. The results indicate that implementing measures to reduce the influence of rape myths on judges' evaluations in rape trials could lead to fairer court decisions.
ABO*cisAB allele with unusual phenotype in a Brazilian family
Authors: Miola Marcos Paulo , Muniz Janaína Guilhem , Santos Flávia Leite Souza , Ricci‐Junior Octávio , de Mattos Luiz Carlos 
Published: December 2024

AbstractBackgroundAmong the alleles of the ABO system, cisAB and B(A) are the most intriguing due to their ability to encode a glycosyltransferase that can synthesize both A and B antigens. This dual activity leads to the formation of the AB phenotype, even in the presence of the O allele; resolution is achieved by molecular analyses.Case Presentation and MethodsWe describe herein a Brazilian family in which the mother (M42.1) of group AB and the father (M42.2) of group O have two children of group AB (M42.3 and M42.4). Serological characterization involved ABO and H phenotyping tests and serial dilution of ABO monoclonal antibodies. Characterization of ABO genotypes and alleles were performed by PCR‐RFLP and sequencing.Results and DiscussionIn serological tests, red blood cells from M42.1, M42.3, and M42.4 showed an intermediate reactivity pattern between A1B and A2B. Molecular analyses revealed the presence of the ABO*O.01.01/O.01.01 genotype in M42.2 and the ABO*cisAB.05/O.01.01 genotype in M42.1, M42.3, and M42.4. The ABO*cisAB.05 allele encodes a glycosyltransferase able to synthesize A and B antigens in quantities sufficient to cause an agglutination reaction higher than that observed in A2B phenotypes.ConclusionThe combination of serological and molecular methods used in this study allowed us to determine the serological pattern, identify the ABO alleles, and explain the inheritance of the AB phenotype in this family.
Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage
Authors: Liu Zhenghua , Jiang Chengying , Yin Zhuzhong , Ibrahim Ibrahim Ahmed , Zhang Teng , Wen Jing , Zhou Lei , Jiang Guoping , Li Liangzhi , Yang Zhendong , Huang Ye , Yang Zhaoyue , Gu Yabing , Meng Delong , Yin Huaqun 
Published: December 2024

ABSTRACT

Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (
r
= −0.518,
P
= 0.007) and dissolved oxygen (
r
= 0.471,
P
= 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.

IMPORTANCE
Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.
On professional mutualism: a blueprint for early-career virologists
Authors: Shah Priya S. 
Published: December 2024

ABSTRACT

Are you an early-career virologist looking for an independent position? Are you searching for the right home for your lab and not sure what you are looking for? I am here to tell you that the right professional home may not be what you expected. The key is to find a home that offers professional mutualism—it allows you and your home department to grow in new directions and hopefully thrive in the process.
CD6 regulates CD4 T follicular helper cell differentiation and humoral immunity during murine coronavirus infection
Authors: Cardani-Boulton Amber , Lin Feng , Bergmann Cornelia C. 
Published: December 2024

ABSTRACT

During activation, the T cell transmembrane receptor CD6 becomes incorporated into the T cell immunological synapse where it can exert both co-stimulatory and co-inhibitory functions. Given the ability of CD6 to carry out opposing functions, this study sought to determine how CD6 regulates early T cell activation in response to viral infection. Infection of CD6-deficient mice with a neurotropic murine coronavirus resulted in greater activation and expansion of CD4 T cells in the draining lymph nodes. Further analysis demonstrated that there was also preferential differentiation of CD4 T cells into T follicular helper cells, resulting in accelerated germinal center responses and emergence of high-affinity virus-specific antibodies. Given that CD6 conversely supports CD4 T cell activation in many autoimmune models, we probed potential mechanisms of CD6-mediated suppression of CD4 T cell activation during viral infection. Analysis of CD6 binding proteins revealed that infection-induced upregulation of
Ubash3a
, a negative regulator of T cell receptor (TCR) signaling, was hindered in CD6-deficient lymph nodes. Consistent with greater T cell activation and reduced UBASH3a activity, the T cell receptor signal strength was intensified in CD6-deficient CD4 T cells. These results reveal a novel immunoregulatory role for CD6 in limiting CD4 T cell activation and deterring CD4 T follicular helper cell differentiation, thereby attenuating antiviral humoral immunity.

IMPORTANCE

CD6 monoclonal blocking antibodies are being therapeutically administered to inhibit T cell activation in autoimmune disorders. However, the multifaceted nature of CD6 allows for multiple and even opposing functions under different circumstances of T cell activation. We therefore sought to characterize how CD6 regulates T cell activation in the context of viral infections using an
in vivo
murine coronavirus model. In contrast to its role in autoimmunity, but consistent with its function in the presence of superantigens, we found that CD6 deficiency enhances CD4 T cell activation and CD4 T cell help to germinal center-dependent antiviral humoral responses. Finally, we provide evidence that CD6 regulates transcription of its intracellular binding partner UBASH3a, which suppresses T cell receptor (TCR) signaling and consequently T cell activation. These findings highlight the context-dependent flexibility of CD6 in regulating
in vivo
adaptive immune responses, which may be targeted to enhance antiviral immunity.
Stage-specific function of sphingolipid synthases in African trypanosomes
Authors: Heise Norton , Koeller Carolina M. , Sharif Mohamed , Bangs James D. 
Published: December 2024

ABSTRACT

The protozoan parasite
Trypanosoma brucei
is the only known eukaryote capable of synthesizing the three main phosphosphingolipids: sphingomyelin (SM), inositol phosphorylceramide (IPC), and ethanolamine phosphorylceramide (EPC). It has four paralogous genes encoding sphingolipid synthases (
TbSLS1–4
). TbSLS1 is a dedicated IPC synthase, TbSLS2 is a dedicated EPC synthase, and TbSLS3 and TbSLS4 are bifunctional SM/EPC synthases. IPC synthesis occurs exclusively in the procyclic insect stage (PCF), EPC is limited to the mammalian bloodstream form (BSF), and SM is synthesized throughout the life cycle. TbSLSs are indispensable for the viability of BSF and are, thus, potential drug targets. The relative stage-specific expression of each
TbSLS
paralog was compared, and the results match phosphosphingolipid content. Induction of pan-specific RNAi silencing was lethal in both BSF and PCF. To investigate individual TbSLS functions, separate HA-tagged genes, recoded to be RNAi-resistant (RNAi
R
), were engineered to replace a single allele of the entire
TbSLS
locus within parental BSF and PCF RNAi cell lines. RNAi
R
TbSLS3
and
TbSLS4
both rescued BSF growth under silencing. Expression of RNAi
R
TbSLS1
, normally repressed in BSF, did not rescue BSF viability but was not detrimental to normal
in vitro
growth. RNAi
R
TbSLS1
,
TbSLS3
, and
TbSLS4
were each sufficient to rescue PCF growth, indicating IPC is not essential for PCF viability
in vitro
. All TbSLSs localize to distal Golgi compartments in both BSF and PCF cells. These findings raise interesting questions about the roles of individual phosphosphingolipids in
in vivo
infection of the mammalian and tsetse hosts.

IMPORTANCE
African trypanosomes are eukaryotic pathogens that cause human and veterinary African trypanosomaisis. Uniquely, they synthesize all three major phosphosphingolipid species using four distinct sphingolipid synthases (SLS). This work details the function of each SLS in both bloodstream and insect form parasites. Novel and unexpected sphingolipid dependences are found in each stage. These results are consistent with this metabolic pathway being a valid target for chemotherapeutic intervention.
Genome sequences of
Staphylococcus aureus
RN4220
Authors: Ko Eon-Min , Kim Seonghan 
Published: December 2024

ABSTRACT

In this study, we present whole genome sequences of
Staphylococcus aureus
RN4220. Using PacBio DNA sequencing and
de novo
assembly, we obtained a single contig of 2,697,647 bp, which includes 2,652 predicted genes comprising protein-coding sequences, tRNAs, and rRNAs.
Whole-genome sequencing of three extremophile
Bacillus
sp. strains isolated from the Atacama Desert
Authors: Cavanaugh Nicole T. , Kumar Girish , Couto Frignani Matteo , Thewedros Nathan , Twahirwa Marcello , Riquelme Carlos , Hudson André O. , Chai Yunrong , Godoy-Carter Veronica 
Published: December 2024

ABSTRACT

The Atacama Desert is home to bacteria that use biofilms as a means of protecting themselves against the harsh environment. To inform research regarding this survival mechanism, we cultured and sequenced the genomes of three
Bacillus
sp. isolates from Atacama Desert soil.
Draft genome sequence of
Aureobasidium pullulans
ATCC15233
Authors: Li Shuang , Wu Xiuyun , Meng Jing 
Published: December 2024

ABSTRACT

Aureobasidium pullulans
is a well-studied polyextremotolerant generalist fungus with a ubiquitous distribution, which can efficiently secret extracellular polysaccharides, especially pullulan. Here, we reported the draft genome of
A. pullulans
ATCC15233, whose genome length is 30,444,007 bp, with a GC content of 50.63%.
Genome sequence of
Bradyrhizobium
sp. Ash2021, a free-living
Bradyrhizobium
species isolated from
Pinus radiata
forest soil
Authors: Armstrong Charlotte , Wakelin Steve 
Published: December 2024

ABSTRACT

Bradyrhizobium
sp. Ash2021 is a free-living soil bacterium isolated from a
Pinus radiata
forest in Canterbury, New Zealand. The genome comprises of a 9,328,819 bp chromosome and a 375,468 bp plasmid. The chromosome harbors biosynthesis pathways for auxins, thiazole-oxazole-modified microcins, and polyketide synthase. The plasmid harbors lactate and GlcNAc metabolism genes.
Whole-genome sequencing of novel pathogenic and multidrug-resistant
Kytococcus sedentarius
, causing mortality in fish species (
Labeo rohita
)
Authors: Das Basanta Kumar , Kumar Vikash , Roy Suvra , Mohanty Debasmita , Jana Asim Kumar , Gadnayak Ayushman 
Published: December 2024

ABSTRACT

We present a novel pathogenic and multidrug-resistant
Kytococcus sedentarius
isolated from
Labeo rohita
. The bacterium belongs to the Micrococcales order and has a genome consisting of 2.59 Mb in length and 71.7% GC content.
K. sedentarius
contains 2,393 coding gene sequences, 6 rRNA, 51 tRNA, 1 tmRNA, and 2,173 antimicrobial resistance genes.
Complete genome sequence of strain AEG42_29 (DSM 112329), a member of the genus
Paraconexibacter
isolated from soil
Authors: Vieira Selma , Huber Katharina , Geppert Alicia , Overmann Jörg 
Published: December 2024

ABSTRACT

We report the complete genome sequence of strain AEG42_29, a representative of the genus
Paraconexibacter
isolated from a temperate grassland soil. Its genome codes for several genes involved in stress response, defense, and virulence, which may help this bacterium cope with fluctuating conditions in the soil environment.
Detectability and cortical depth dependence of stimulus-driven high-frequency BOLD oscillations in the human primary somatosensory and motor cortex
Authors: Hodono Shota , Polimeni Jonathan R. , Reutens David , Cloos Martijn A. 
Published: December 2024

Abstract
In functional magnetic resonance imaging (fMRI), neural activity is inferred from the associated hemodynamic response. However, the degree to which hemodynamics can track dynamic changes in neuronal activity, and thus the ultimate temporal resolution of fMRI, remains unknown. To evaluate the detectability of stimulus-driven high-frequency blood oxygenation level dependent (BOLD) signal oscillations in functionally and vascularly distinct cerebral cortical areas, stimuli up to 0.5 Hz were used to evoke activation in the primary somatosensory and motor cortex. Despite their functional and vascular differences, a similar frequency dependence was observed in both cortical areas. We then proceeded to investigate these signals at different levels of the cortical vascular hierarchy, using cortical depth as a proxy. We observed that, above 0.33 Hz, the BOLD response amplitude decreased faster with increasing frequency near the pial surface than in the parenchyma, suggesting that, in addition to exhibiting high spatial specificity, parenchymal signals—accessible with high spatial resolution imaging—also attenuate less rapidly when the stimulus frequency is increased. In addition, as the stimulus frequency increased, we observed larger relative phase differences in the BOLD oscillations across cortical depths. When averaged across depths, these signals can thus interfere destructively, suggesting that high spatial resolutions can avoid this phase cancellation and thereby aid in the detection of rapid BOLD oscillations.
Morphological redescription and population genetics of Pagastia (Pagastia) orientalis (Tshernovskij, 1949) (Diptera: Chironomidae: Diamesinae)
Authors: SEMENCHENKO ALEXANDER A. , YAGODINA VIKTORIIA D. , SELIVERSTOV NIKITA A. , MAKARCHENKO EUGENYI A. 
Published: December 2024

Pagastia (P.) orientalis (Tshernovskij, 1949) is redescribed by morphology of adult male from East Palaearctic with remarks on some variability of morphological features and with consideration of population genetics of species, namely population structure and variability from 24 localities belonging to 10 groups. Population genetic analysis of P. (P.) orientalis revealed multiple haplotypes (209 haplotypes for 213 samples) and a high level of haplotype diversity—0.999±0.001. The results of neutrality tests were significant (P<0.01) and showed negative values, which may indicate population expansion in the past. Clustering of haplotypes into haplogroups was shown, the differentiation between which is significant (P<0.001) while the gene flow was almost virtually absent, which may affect at the level of genetic diversity of a single population.
Clinical Characteristics and Risk Factors for Persistent Thrombocytopenia among Pediatric Patients after Bone Marrow Transplant in Saudi Arabia: A 3-Year Retrospective Observational Analysis from Tertiary Hospital
Authors: Kanan Mohammed , Almotairi Abdullah , Alrumaih Faisal , Hammad Reem , Almotairi Mohammed 
Published: December 2024

Background Bone marrow transplantation (BMT) is a crucial treatment for pediatric patients with various hematological, oncological, and genetic diseases. However, persistent thrombocytopenia (PT) post-transplantation poses a significant challenge, affecting recovery and prognosis. Purpose This study aimed to identify the clinical characteristics and risk factors associated with PT in pediatric patients post-BMT, specifically in Saudi Arabia. Methods A retrospective cohort study design was employed, involving pediatric patients who underwent BMT between January 2020 and January 2023. Clinical characteristics, laboratory results, treatment data, and outcomes were collected from electronic medical records. Logistic regression analyses were conducted to identify risk factors associated with PT. Results Among the 77 pediatric patients in the study, no significant differences were observed in demographic characteristics, transplant types, or treatment modalities between early-onset and late-onset thrombocytopenia groups. However, the duration of thrombocytopenia post-transplant differed significantly between the groups, with early-onset cases experiencing shorter durations. Infections and graft-versus-host disease were common post-transplant complications. Chemotherapy and antiviral therapy were frequently administered treatments. Pediatric patients undergoing BMT are susceptible to PT, with varying durations based on the onset timing. Conclusion The study emphasizes the importance of risk assessment and tailored management to mitigate thrombocytopenia in pediatric BMT patients. Further research is needed to elucidate the underlying mechanisms and optimize therapeutic interventions for thrombocytopenia in this population.
Allergen immunotherapy
Authors: Boursiquot Jean-Nicolas , Gagnon Rémi , Quirt Jaclyn , Ellis Anne K. 
Published: December 2024

AbstractAllergen immunotherapy (AIT) is a potentially disease-modifying therapy that is effective for the treatment of allergic rhinitis/conjunctivitis, allergic asthma and stinging insect hypersensitivity. The decision to proceed with AIT should be made on a case-by-case basis, based on a comprehensive evaluation of the patient, allergy testing and a thorough discussion with the patient about treatment goals, risks vs. benefits, and long-term commitment to the treatment plan. For those with allergic rhinitis and/or asthma, it is also important to consider individual patient factors, such as the degree to which symptoms can be reduced by avoidance measures and pharmacological therapy, the amount and type of medication required to control symptoms, the adverse effects of pharmacological treatment, and patient preferences.Since AIT is associated with a risk of anaphylaxis, it should only be prescribed by physicians who are adequately trained in the treatment of allergic conditions. Furthermore, for subcutaneous therapy, injections must be given under medical supervision in clinics that are equipped to manage anaphylaxis. In this article, we review the indications and contraindications, patient selection criteria, and details regarding the administration, safety and efficacy of AIT for allergens other than foods. Immunotherapy for food allergy will be discussed in the Oral Immunotherapy article in this supplement.
Antibiotic prophylaxis in oral implant surgery in Germany: a cross-sectional study
Authors: Peter Jens-Uwe , Ladewig Johannes , Stoll Christian , Zolk Oliver 
Published: December 2024

Abstract
Purpose
Prophylactic antibiotics are used in dental implants to reduce infection risk and implant failure, especially benefiting patients with risk factors. However, evidence suggests that using clindamycin or extending antibiotics postoperatively has an unfavorable risk–benefit ratio.

Methods
This national cross-sectional study analyzed antibiotic prophylaxis during implant insertion across Germany. Dentists from the German Society for Oral Implantology (DGOI) provided demographic information and data on the next 10 consecutive implant patients, including age, sex, risk factors, type of implantation, and antibiotic details.

Results
103 dentists participated, providing data on 1040 patients. Most dentists were male and aged 30–64. Patients were evenly split between genders, with an average age of 51 years. Antibiotics were administered in 87.6% of all cases, more frequently for patients undergoing bone augmentation (OR 7.01, p < 0.0001), immediate (OR 3.11, p = 0.002) or delayed (OR 5.30, p < 0.0001) implant insertion, and those with cardiovascular disease (OR 3.24, p = 0.009). 74.8% of implantologists tended to use antibiotic prophylaxis routinely, while the remaining implantologists decided on a case-by-case basis. Implantologists primarily used aminopenicillins for 63.8% of prescriptions and clindamycin for the remaining 35.6%. Additionally, 78.8% of patients with prophylaxis received postoperative, multi-day treatments.

Conclusions
The study reveals extensive antibiotic use for perioperative prophylaxis in implant surgery, often not justified by current recommendations, particularly concerning the choice of antibiotic (e.g., clindamycin) and duration (e.g., postoperative use). Specialized clinical guidelines and targeted training for dentists on antibiotic prophylaxis are needed.

Graphical Abstract