bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of the Gamma-Ray Bursts Prompt Emission Under the Relativistically Expanding Fireball Scenario
Authors: Gupta Soumya , Sahayanathan Sunder 
Published: July 2024

Abstract
The spectral properties of a composite thermal emission arising from a relativistic expanding fireball can be remarkably different from the Planck function. We perform a detailed study of such a system to explore the features of the prompt emission spectra from gamma-ray bursts (GRBs). In particular, we address the effect of optical opacity and its dependence on the density profile between the expanding gas and the observer. This results in a nontrivial shape of the photospheric radius, which in combination with the constraints derived from the equal arrival time can result in a mild broader spectrum compared to the Planck function. Further, we show the time-integrated spectrum from the expanding fireball deviates significantly from the instantaneous emission and is capable of explaining the observed broad spectral width of GRBs. We also show that the demand of the spectral width of the order of unity, obtained through statistical analysis, is consistent with the scenario where the dynamics of the expanding fireball are governed predominantly by the energy content of the matter.
An annotated and illustrated identification guide to common mesophotic reef sponges&nbsp;(Porifera, Demospongiae, Hexactinellida, and&nbsp;Homoscleromorpha) inhabiting Flower Garden Banks national marine sanctuary and vicinities
Authors: Díaz María Christina , Nuttall Marissa , Pomponi Shirley , Rützler Klaus , Adams Christi , Hickerson Emma , Schmahl George , Ward Klontz Sarah 
Published: July 2024

Sponges are recognized as a diverse and abundant component of mesophotic and deep-sea ecosystems worldwide. In Flower Garden Banks National Marine Sanctuary region within the northwestern Gulf of Mexico, sponges thrive among diverse biological and geological habitats between 16-200+ m deep (i.e., coral reefs and communities, algal nodule and coralline algae reefs, mesophotic reefs, patch reefs, scarps, ridges, soft substrate, and rocky outcrops). We present a synoptic guide developed by studying common sponge species in the region, through direct sampling and in situ photographic records. A total of 63 species are included: 60 are Demospongiae (14 orders), 2 are Hexactinellida (1 order), 2 are Homoscleromorpha (1 order). Thirty-nine taxa are identified to species and 11 were identified to have affinity with, but are not identical to, a known species. Thirteen taxa could only be identified to genus level at this time, and the species remain as uncertain (incerta sedis), with the potential to constitute new species or variants of known species. One specimen received only a family assignation. This study extends geographic or mesophotic occurrence data for 11 known species and includes several potentially new species. This work improves our knowledge of Gulf of Mexico sponge biodiversity and highlights the importance of the region for scientists and resource managers.
New distributional records of Southern Ocean Isopoda based on vouchers from the Italian National Antarctic Museum (MNA, Section of Genoa)
Authors: Noli Nicholas , Cecchetto Matteo , Guzzi Alice , Grillo Marco , Cometti Valentina , Schiaparelli Stefano 
Published: July 2024

The order Isopoda Latreille, 1816 consists of species occurring in terrestrial, marine and freshwater environments. In the Southern Ocean (SO), this group is amongst the most speciose and occur at all depths. Isopoda biogeography, despite being studied since the first Antarctic expeditions, is still poorly known from a geographical point of view and shows large occurrence gaps for some groups in specific sectors of the SO. In this paper, we update the isopod checklists of the Ross Sea (RS) and of some peri-Antarctic areas, such as the South Orkney Islands (SOI) and the South Sandwich Islands (SSI), based on the study of museum vouchers curated by the Italian National Antarctic Museum (MNA, Section of Genoa).
A total of 279 MNA samples from 15 different expeditions were studied. From this material, consisting of 419 specimens, 41 accepted species distributed in 24 families and 51 genera were identified. Comparing this newly-obtained information with the GBIF (Global Biodiversity Information Facility) and OBIS (Ocean Biodiversity Information System) portal, 15 species are here reported for the first time in the Ross Sea, with five new records in the Ross Sea Marine Protected Area. All records are new for the Terra Nova Bay area, for which a checklist of this group has never been produced before.
Ibn Khaldûn, une source historique majeure l’apport du Kitâb al-‘Ibar à la connaissance de l’ethnonymie berbère
Authors: M’Charek Ahmed 
Published: July 2024

L’« édition Chabbouh » du Kitâb al-‘Bar (ou Livre des Exemples ) d’Ibn Khaldûn (Tunis, 2006-2015) a mis à la disposition des chercheurs une copie du « manuscrit du Caire » (conservé à Istanbul), qui comporte les signes diacritiques et les digrammes (éléments essentiels pour l’étude de la phonétique berbère). Les chapitres berbères de cet ouvrage contiennent en outre une information précieuse sur les grandes tribus berbères attestées par les sources médiévales (Kutâma, Sanhâja, Haouara, Zanâta, Maghrâwa…). Dans la substantielle notice consacrée aux Zanâta par exemple, l’auteur du XIV e siècle explique l’étymologie de l’ethnonyme porté par ce peuple (nom de l’ancêtre éponyme, Jâna, et le paradigme onomastique qui en découle : Zâna/Zanat, Iznaten et Zanata) ; de même qu’il y souligne l’antiquité du peuplement zénète en donnant les aires d’habitat de ses principales branches tribales (Jarâwa, Maghrâwa, Banu Ifren). L’examen croisé des sources antiques et médiévales a permis de montrer le bien-fondé du témoignage d’Ibn Khaldûn (identification du pays zénète de l’Aurès depuis la principauté des Avares (Haouara) et Dianenses ( Zanâta ) dans l’Aurès et le Hodna, attestée par les sources latines du V e siècle (Victor de Vita notamment). Parce qu’il contient les clés de l’ethnonymie berbère, le maître-livre d’Ibn Khaldûn constitue, selon moi, une source incontournable pour l’étude de la continuité du peuplement au Maghreb, de l’Antiquité au Moyen Âge (une continuité déjà établie pour des dizaines d’ethnonymes libyco-berbères grâce aux résultats récents de la recherche spécialisée).
The X-files
Authors: Méndez Dosuna Julián V. 
Published: July 2024

The⁠⁠⁠ ⁤⁤letter X stands for [ks] in the Greek “dark blue” scripts, and for /⁠kh/ in the “red” scripts. Moreover, the sequence [ks] is usually spelt with the digraph ΧΣ in the “light blue” scripts, rather than with expected ΚΣ (ΧΣΕΝΟΣ). Several phonetic explanations have been proposed to account for this fact, but none of them proves satisfactory. Furthermore, the spelling ΧΣ is purportedly attested in some “red” scripts (Boeotian ΑΡΓΥΡΟΤΟΧΣΟΙ = ἀργυροτόξωι), in which the letter X or the digraph ▯Σ should be expected. To complicate matters further, a spelling ▯Σ, usually interpreted as a variant of “light blue” ΧΣ, occurs at Naxos (NA▯ΣIO). This paper tries to integrate all these seemingly disparate facts into a principled explanation. “Dark blue” Ξ, Naxian ▯Σ, and “red” Χ are probably all avatars of Phoenician samek, and the use of X for /⁠kh/ in the “blue” scripts resulted from a misanalysis of pleonastic ΧΣ spellings.
Testicules, masculinités et normes de genre. Les récits scientifiques français sur les castrats italiens au siècle des Lumières
Authors: Hanafi Nahema 
Published: July 2024

Peu présents dans la France des Lumières, les castrats italiens n’en deviennent pas moins un sujet de discussion scientifique dans le royaume en ce qu’ils incarnent un eunuchisme occidental. Mobilisée pour penser les limites éthiques du geste chirurgical, la castration musicale s’invite dans différents traités, de manière développée ou plus anecdotique, et renvoie à de multiples questionnements relatifs aux normes corporelles, aux identités de genre, aux capacités reproductives ou à la sexualité. Cet article s’emploie à observer la façon dont le tableau physique et moral des castrats élaboré par les médecins et les naturalistes français des Lumières s’inscrit dans l’effort de construction et de définition médicale du sexe en s’attachant plus particulièrement à fixer les normes du masculin. Au cours de la seconde moitié du xviiie siècle en particulier, la figure du castrat sert de support à l’énonciation des caractéristiques physiques et morales d’une masculinité hégémonique « à la Française » et, partant, des contours d’une masculinité subordonnée (italienne, méridionale, orientale) dont les chanteurs seraient l’incarnation.
Protective Non-neutralizing anti–N-terminal Domain mAb Maintains Fc-mediated Function against SARS-COV-2 Variants up to BA.2.86-JN.1 with Superfluous In Vivo Protection against JN.1 Due to Attenuated Virulence
Authors: Izadi Arman , Godzwon Magdalena , Söderlund Strand Anna , Schmidt Tobias , Kumlien Georén Susanna , Drosten Christian , Ohlin Mats , Nordenfelt Pontus 
Published: July 2024

Abstract
Substantial evidence supports that Fc-mediated effector functions of anti-spike Abs contribute to anti–SARS-Cov-2 protection. We have previously shown that two non-neutralizing but opsonic mAbs targeting the receptor-binding domain and N-terminal domain (NTD), Ab81 and Ab94, respectively, are protective against lethal Wuhan SARS-CoV-2 infection in K18-hACE2 mice. In this article, we investigated whether these protective non-neutralizing Abs maintain Fc-mediated function and Ag binding against mutated SARS-CoV-2 variants. Ab81 and Ab94 retained their nanomolar affinity and Fc-mediated function toward Omicron and its subvariants, such as BA.2, BA.4, BA.5, XBB, XBB1.5, and BQ1.1. However, when encountering the more heavily mutated BA.2.86, Ab81 lost its function, whereas the 10 new mutations in the NTD did not affect Ab94. In vivo experiments with Ab94 in K18-hACE2 mice inoculated with a stringent dose of 100,000 PFU of the JN.1 variant revealed unexpected results. Surprisingly, this variant exhibited low disease manifestation in this animal model with no weight loss or death in the control group. Still, assessment of mice using a clinical scoring system showed better protection for Ab94-treated mice, indicating that Fc-mediated functions are still beneficial. Our work shows that a protective anti–receptor-binding domain non-neutralizing mAb lost reactivity when BA.2.86 emerged, whereas the anti-NTD mAb was still functional. Finally, this work adds new insight into the evolution of the SARS-CoV-2 virus by reporting that JN.1 is substantially less virulent in vivo than previous strains.
Mycobacterium tuberculosis Utilizes Serine/Threonine Kinase PknF to Evade NLRP3 Inflammasome-driven Caspase-1 and RIPK3/Caspase-8 Activation in Murine Dendritic Cells
Authors: Rastogi Shivangi , Ganesh Akshaya , Briken Volker 
Published: July 2024

Abstract
Dendritic cells (DCs) are crucial for initiating the acquired immune response to infectious diseases such as tuberculosis. Mycobacterium tuberculosis has evolved strategies to inhibit activation of the NLRP3 inflammasome in macrophages via its serine/threonine protein kinase, protein kinase F (PknF). It is not known whether this pathway is conserved in DCs. In this study, we show that the pknF deletion mutant of M. tuberculosis (MtbΔpknF) compared with wild-type M. tuberculosis–infected cells induces increased production of IL-1β and increased pyroptosis in murine bone marrow-derived DCs (BMDCs). As shown for murine macrophages, the enhanced production of IL-1β postinfection of BMDCs with MtbΔpknF is dependent on NLRP3, ASC, and caspase-1/11. In contrast to macrophages, we show that MtbΔpknF mediates RIPK3/caspase-8–dependent IL-1β production in BMDCs. Consistently, infection with MtbΔpknF results in increased activation of caspase-1 and caspase-8 in BMDCs. When compared with M. tuberculosis–infected cells, the IL-6 production by MtbΔpknF-infected cells was unchanged, indicating that the mutant does not affect the priming phase of inflammasome activation. In contrast, the activation phase was impacted because the MtbΔpknF-induced inflammasome activation in BMDCs depended on potassium efflux, chloride efflux, reactive oxygen species generation, and calcium influx. In conclusion, PknF is important for M. tuberculosis to evade NLRP3 inflammasome-mediated activation of caspase-1 and RIPK3/caspase-8 pathways in BMDCs.
Monoclonal Antibodies Engineered with Fc Region Mutations to Extend Protection against Fentanyl Toxicity
Authors: Khaimraj Aaron , Baehr Carly A , Hicks Dustin , Raleigh Michael D , Pravetoni Marco 
Published: July 2024

Abstract
Fentanyl and other synthetic opioids are the leading cause of drug-related deaths in the United States. mAbs that selectively target fentanyl and fentanyl analogues offer a promising strategy for treating both opioid-related overdoses and opioid use disorders. To increase the duration of efficacy of a candidate mAb against fentanyl, we selected three sets of mutations in the Fc region of an IgG1 anti-fentanyl mAb (HY6-F9DF215, HY6-F9DHS, HY6-F9YTE) to increase binding to the neonatal Fc receptor (FcRn). The mAb mutants were compared against unmodified (wild-type [WT], HY6-F9WT) anti-fentanyl mAb for fentanyl binding, thermal stability, and FcRn affinity in vitro, and for efficacy against fentanyl and mAb half-life in vivo in mice. Biolayer interferometry showed a &gt;10-fold increase in the affinity for recombinant FcRn of the three mutant mAbs compared with HY6-F9WT. During an acute fentanyl challenge in mice, all FcRn-mutated mAbs provided equal protection against fentanyl-induced effects, and all mAbs reduced brain fentanyl levels compared with the saline group. Serum persistence of the mutant mAbs was tested in Tg276 transgenic mice expressing human FcRn. After administration of 40 mg/kg HY6-F9WT, HY6-F9DF215, HY6-F9DHS, and HY6-F9YTE, the mAbs showed half-lives of 6.3, 26.4, 14.7, and 6.9 d, respectively. These data suggest that modification of mAbs against fentanyl to bind to FcRn with higher affinity can increase their half-life relative to WT mAbs while maintaining efficacy against the toxic effects of fentanyl, further supporting their potential role as a therapeutic treatment option for opioid use disorder and overdose.
A Case of Listeria Monocytogenes Brain Abscess with a Clinical Presentation Mimicking Stroke
Authors: Chu Ya-Chun , Chen Nai-Ching , Chen Chien-Liang 
Published: July 2024

Purpose:
Kidney transplant recipients are at a high risk of both stroke and infection. We report this case to inform readers of the possibility of the occurrence of Listeria monocytogenes brain abscess despite treatment with low dose trimethoprim–sulfamethoxazole (TMP/SMX).

Case Report:
A 62-year-old man presented to our hospital with right facial palsy, left arm and leg weakness, and mild fever; he was diagnosed with a stroke in the emergency room. The patient had a history of cadaveric renal transplantation 2 years prior, for which he was prescribed tacrolimus- based immunosuppressive drugs. Multiple myeloma was diagnosed 18 months after renal transplant. He was treated with bortezomib and steroids for the multiple myeloma, and low-dose TMP/SMX for pneumocystis prophylaxis. A listeria brain abscess was diagnosed based on a comprehensive medical history, magnetic resonance images, positive blood culture, and brain biopsy. He underwent ampicillin therapy and achieved full recovery after a 3-month follow-up period.

Conclusion:
Physicians should monitor unusual stroke symptoms and consider Listeria brain abscess as a differential diagnosis. This case suggests that listeria brain abscesses can potentially cause temporary neurological deficits akin to a stroke, despite TMP/SMX prophylaxis, but these symptoms resolve without necessitating surgical intervention.
Methodological and TNM Focus-Based Comparison of EGFR Mutation Status in Non-Small-Cell Lung Carcinomas
Authors: Akca Yasemin , Erkilic Suna 
Published: July 2024

Background:
Epidermal growth factor receptor (EGFR) mutations in non-small-cell lung carcinomas (NSCLC) are a frequent class of driver mutations, and tyrosine kinase inhibitor (TKI) therapy provides considerable clinical benefits. Using the most effective and also easiest method for EGFR analysis is cost-effective and time-saving. In this study, we aimed to determine which method could be more effective by comparing the incidences of EGFR mutations in cytological and histological samples which were obtained by different methods also, whether there was a difference in the incidences of EGFR mutations between the primary foci, mediastinal lymph nodes, and distant metastatic foci.

Materials and Methods:
We retrospectively reviewed 420 cases of cytological materials, small biopsies, and surgical samples reported as NSCLC underwent EGFR analysis in our department between 2016 and 2022. We collected the data and interpreted the results from two different perspectives.

Results:
We identified 36 EGFR mutations in 362 biopsies (9.94%) and 17 in 58 cytology samples (29.31%). There is a significant difference between the two methods (P = 0.01*). We observed 38 EGFR mutations in 320 primary foci (11.87%), 7 EGFR mutations in 36 mediastinal or subcarinal lymph nodes (19.44%), and 8 EGFR mutations in 64 distant metastatic foci (12.50%). A significant difference was also observed in pleural samples (P = 0.005*).

Conclusion:
We observed more successful results with cell blocks obtained from liquid-based cytological specimens than with formalin-fixed, paraffin-embedded tissues obtained from resection or otherwise in our clinical routine. Our study results highlight the benefits of cytological specimens in molecular treatments and current therapy modalities.
Utility of Image Morphometry in the Atypical Urothelial Cells and High-Grade Urothelial Carcinoma Categories of the Paris System for Reporting Urinary Cytology
Authors: Sharan K.C. , Rohilla Manish , Dey Pranab , Srinivasan Radhika , Kakkar Nandita , Mavuduru Ravimohan S. 
Published: July 2024

Introduction:
Urinary cytology (UrCy) is highly sensitive to diagnosing high-grade urothelial carcinoma (HGUC) but cannot predict muscularis propria invasion. Further, the atypical urothelial cell category (AUC) may have variable outcomes. Image morphometry (IM) may be a valuable adjunct technique in this setting. Hence, we evaluated IM in the AUC and HGUC categories to improve the diagnostic performance.

Materials and Methods:
The following six nuclear parameters were evaluated by IM on 3150 cells: nucleo-cytoplasmic (N:C) ratio, nuclear area, diameter, perimeter, standard deviation of the nuclear area (SDNA; pleomorphism) and integrated density (ID; nuclear chromasia), using the ImageJ software, in three cohorts based on the histopathology outcome: 20 cases of AUC – benign non-neoplastic outcome (AUC-B); 22 cases of HGUC Muscle invasive (HGUC-MI) and 21 cases of HGUC non-muscle invasive (HGUC-MF).

Results:
A retrospective analysis of urine cytology. The patient’s ages ranged from 36 to 85 years, with a mean age of 60.6. The male-to-female ratio was 5.4:1. A total of 20 cases of AUC-B and 43 cases of HGUC were selected for IM analysis. HGUC cases had higher nuclear parameters than AUC-B, and HGUC-MI had higher SDNA, ID, diameter, and area than HGUC-MF. SDNA and ID predict muscularis propria invasion in HGUC.

Conclusions:
Image morphometry successfully differentiates HGUC cases from benign non-neoplastic ones and might help to identify muscularis propria invasion in HGUC using a combination of nuclear parameters.
Aptima HPV Genotypes in Abnormal Cervical Samples in Different Age Groups – Implication on Vaccination Strategies
Authors: Al-Awadhi Rana , AlRoomy Moody , Dashti Hawraa , Kapila Kusum 
Published: July 2024

Context:
Persistent infection with high-risk human papillomavirus (hr-HPV) types is associated with high-grade cervical abnormalities.

Aims:
The aim of the study was to find most hr-HPV types causing persistent infection in abnormal cytological samples using Aptima HPV testing and discuss the compatibility of the Gardasil 9 vaccine in targeting most types.

Settings:
The study was conducted in a cytology laboratory in a tertiary hospital.

Design:
This is a retrospective observational study.

Methods and Materials:
Cytology and HPV Aptima test reports were obtained for abnormal cervical samples for a 6-year period.

Statistical Analysis Used:
Pearson Chi-square test.

Results:
Reports of 2834 abnormal cervical samples were analyzed. Aptima testing was positive in 21% of samples, including 92% of squamous cell carcinoma (SCC), 76.4% of the high-grade squamous intraepithelial lesion (HSIL), 52% of low-grade squamous intraepithelial lesion (LSIL), 40% of adenocarcinoma (ADC), and 21% of atypical squamous cells that cannot exclude HSIL (ASC-H). The Aptima other hr-HPV group was most common (60%), HPV16 was 26%, HPV18/45 was 9.6%, and double HPV infection was 4.3%. HPV16 was the most common infection in HSIL+ cases. HPV infection was most common in age groups (30–39) and (40–49), and a shift to age groups (50–59) and ≥60 was seen in HSIL+ cases.

Conclusions:
This study is the first of its kind in correlating age with hr-HPV and cytology findings in the Middle East and adds to previous knowledge related to the prevalence and Aptima testing of HPV. The outcome could be used as a baseline for the Gardasil 9 vaccine and for the assessment of its effectiveness after three or five years from initiation.
The Influence of Environmental Factors on Photosynthesis - Learning Design and Assessment Plan for a STEM Curriculum
Authors: Yuxuan Liu  
Published: July 2024

There has been a lot of attention on STEM education, but there is less STEM curriculum for teachers to have a reference point in China. The article proposes a short STEM curriculum for use by teachers in the teaching of the STEM curriculum. The curriculum is for 10th graders. Biology is the main subject integrated with mathematics and chemistry. The article shows specific course content, including 3 different experiments. Experiments in which students participate independently are more likely to sharpen their thinking. Inquiry-based learning is adopted as the educational approach, through which students can discover new causal relationships because students formulate hypotheses and test them by conducting experiments and observations. Additionally inquiry-based learning encourages students to think logically, critically, and analytically, which is helpful in increasing students’ critical thinking. Critical thinking is reasonable and reflective thinking focused on what to believe or do. Students with critical thinking skills can achieve incredible learning outcomes because they can consciously control their goals and attention. There are six dimensions of critical thinking, based on the assignment—experimental report, analysis dimension and explanation dimension will be assessed.