bluuebunny/crossref_metadata_2025_split huggingface dataset:
Near-full-length genome sequences of human norovirus GI.7[P7] and GII.4[P31] strains co-infecting a California patient in 2017
Authors: Yang Zhihui , Mammel Mark , Wolfe Julia 
Published: September 2023

ABSTRACT
Accurate identification of human noroviruses (HuNoVs) from outbreaks or sporadic cases is critical for source tracing and outbreak investigation. Whole-genome sequencing is a powerful tool for the detection, identification, and discrimination of HuNoV strains. We report here the nearly complete genome sequences of GI.7[P7] and GII.4[P31] strains detected in a Californian patient co-infected by both strains in 2017.
Stable microbial community in compacted bentonite after 5 years of exposure to natural granitic groundwater
Authors: Engel Katja , Ford Sian E. , Binns W. Jeffrey , Diomidis Nikitas , Slater Greg F. , Neufeld Josh D. 
Published: September 2023

ABSTRACT

The Materials Corrosion Test (MaCoTe) at the Underground Research Laboratory in Grimsel, Switzerland, assesses the microbiology and corrosion behavior of engineered barrier components of a deep geological repository (DGR) for long-term disposal of high-level nuclear waste. Diversity and temporal changes of bentonite-associated microbial community profiles were assessed under DGR-like conditions for compacted Wyoming MX-80 bentonite (1.25 g/cm
3
and 1.50 g/cm
3
targeted dry densities) exposed to natural groundwater. Using culture-dependent and molecular techniques, samples taken from the outside layer of 5-year borehole modules revealed up to 66% and 23% of 16S rRNA gene sequences affiliated with
Desulfosporosinus
and
Desulfovibrio,
respectively. Putatively involved in sulfate reduction, these taxa were almost undetectable within the bentonite core. Instead, microbial profiles of the inner bentonite core were similar to uncompacted bentonite used to pack modules years earlier, and were consistent with a previously published 1-year time point, revealing no detectable microbial growth. Abundances of culturable aerobic and anaerobic heterotrophic bacteria in the uncompacted bentonite were relatively low, with less than 1,000 and 100 colony-forming units (CFUs) per gram dry weight, respectively. Nearly 5 years after emplacement, culturable heterotrophic bacterial CFUs and sulfate-reducing bacteria did not change significantly inside the bentonite core. Phospholipid fatty acid data indicated similar lipid abundance, and corresponding cell abundance estimates, for inner 5-year MaCoTe bentonite samples compared to those previously obtained for 1-year incubations. Collectively, our results provide complementary evidence for microbial stability inside highly compacted bentonite exposed to conditions that mimic engineered barrier components of a deep geological repository.

IMPORTANCE

The long-term safety of a deep geological repository for used nuclear fuel is dependent on the performance of the engineered and natural barriers. Microbial activity can produce chemical species that can influence the corrosion of the disposal containers for used nuclear fuel. Although previous studies have evaluated the microbiology of compacted bentonite clay within subsurface environments, these have been limited to relatively short incubations (i.e., 1 year). The current study provides a unique 5-year perspective that reinforces previous findings of growth inhibition for bentonite clay exposed to
in situ
subsurface conditions.
The First Record of a Representative of the Toarcian–Early Aalenian Belemnites in Kimberlites of the Obnazhennaya Pipe (Northeastern Siberian Platform)
Authors: Dzyuba O. S. , Grinenko V. S. , Oshchepkova M. G. , Shurygin B. N. 
Published: September 2023

Abstract
A rostrum fragment of a representative of the Toarcian–Early Aalenian (the latest Early Jurassic–the earliest Middle Jurassic) belemnites Arcobelus cf. krimholzi (Sachs, 1970) was found for the first time in kimberlites of the Obnazhennaya pipe of the Kuoika kimberlite field (northeastern Siberian Platform, Olenek Uplift). It was shown that the belemnite records previously known here and dated to the Late Jurassic or Early Cretaceous may be of Bajocian–Bathonian (Middle Jurassic) age. The stage of kimberlite magmatism of 177 ± 1.5 Ma, recently established in the northeastern part of the Siberian craton according to U–Pb geochronological data, falls on the time of the existence of belemnites of the genus Arcobelus. The estimated Late Bajocian–Early Bathonian age of the representative of the genus Pachyteuthis, previously found in kimberlites of the Obnazhennaya pipe, is consistent with the 40Ar/39Ar age (167 Ma), as well as with the age based on some paleomagnetic data (168 ± 11 Ma) reported for the pipe. Taking into consideration the new data on belemnites, the internal part of the shelf should be extended to the territory of the Kuoika kimberlite field in the paleogeographic schemes of the northeastern part of the Siberian Platform during the Toarcian–Early Bathonian.
Incidence rate of injury and injury sites in European and Swiss karate competitions: a prospective epidemiological study of 2404 fights
Authors: Rosso Claudio , Arnold Roland F , Daci Armond , Grezda Kushtrim 
Published: September 2023

ObjectivesTo compare the rates and injury sites among competitors in European and Swiss karate tournaments and to identify differences in these incidence rates by sex and age.MethodsThis prospective cohort study collected data from two European and four national tournaments in Switzerland between 2011 and 2019. The on-site medical staff completed an anonymised report sheet with demographic data and injury characteristics in all injuries requiring medical treatment. The incidence rates per 1000 exposed athletes (AoE) and 1000 min of exposition (MoE) were analysed. Furthermore, the relative risk of injury related to sex and age was calculated and compared.ResultsIn total, 228 injuries were observed in 2404 fights, for an incidence rate of 47.4 per 1000 AoE (95% CI 41.5 to 54.0) or 22.5 injuries per 1000 MoE (95% CI 19.7 to 25.6), respectively. The oldest age group (senior) of both sexes had a 3.6-fold (95% CI 2.7 to 4.8) significantly higher relative risk of injury than younger participants. Furthermore, there was a 2.9-fold (95% CI 1.6 to 5.6) statistically higher risk of injury for males in the senior age group compared with senior females. The most injured body part was the head, followed by the lower extremity, trunk and upper extremity.ConclusionSenior athletes, especially senior males, had significantly more injuries compared with younger and female senior competitors. Medical staff should be aware of the increased propensity for injury among this age and sex group to facilitate injury prevention and intervention.
The landscape of MHC-presented phosphopeptides yields actionable shared tumor antigens for cancer immunotherapy across multiple HLA alleles
Authors: Molvi Zaki , Klatt Martin G , Dao Tao , Urraca Jessica , Scheinberg David A , O'Reilly Richard J 
Published: September 2023

BackgroundCertain phosphorylated peptides are differentially presented by major histocompatibility complex (MHC) molecules on cancer cells characterized by aberrant phosphorylation. Phosphopeptides presented in complex with the human leukocyte antigen HLA-A*02:01 provide a stability advantage over their non-phosphorylated counterparts. This stability is thought to contribute to enhanced immunogenicity. Whether tumor-associated phosphopeptides presented by other common alleles exhibit immunogenicity and structural characteristics similar to those presented by A*02:01 is unclear. Therefore, we determined the identity, structural features, and immunogenicity of phosphopeptides presented by the prevalent alleles HLA-A*03:01, HLA-A*11:01, HLA-C*07:01, and HLA-C*07:02.MethodsWe isolated peptide-MHC complexes by immunoprecipitation from 11 healthy and neoplastic tissue samples using mass spectrometry, and then combined the resulting data with public immunopeptidomics data sets to assemble a curated set of phosphopeptides presented by 96 samples spanning 20 distinct healthy and neoplastic tissue types. We determined the biochemical features of selected phosphopeptides by in vitro binding assays and in silico docking, and their immunogenicity by analyzing healthy donor T cells for phosphopeptide-specific multimer binding and cytokine production.ResultsWe identified a subset of phosphopeptides presented by HLA-A*03:01, A*11:01, C*07:01 and C*07:02 on multiple tumor types, particularly lymphomas and leukemias, but not healthy tissues. These phosphopeptides are products of genes essential to lymphoma and leukemia survival. The presented phosphopeptides generally exhibited similar or worse binding to A*03:01 than their non-phosphorylated counterparts. HLA-C*07:01 generally presented phosphopeptides but not their unmodified counterparts. Phosphopeptide binding to HLA-C*07:01 was dependent on B-pocket interactions that were absent in HLA-C*07:02. While HLA-A*02:01 and HLA-A*11:01 phosphopeptide-specific T cells could be readily detected in an autologous setting even when the non-phosphorylated peptide was co-presented, HLA-A*03:01 or HLA-C*07:01 phosphopeptides were repeatedly non-immunogenic, requiring use of allogeneic T cells to induce phosphopeptide-specific T cells.ConclusionsPhosphopeptides presented by multiple alleles that are differentially expressed on tumors constitute tumor-specific antigens that could be targeted for cancer immunotherapy, but the immunogenicity of such phosphopeptides is not a general feature. In particular, phosphopeptides presented by HLA-A*02:01 and A*11:01 exhibit consistent immunogenicity, while phosphopeptides presented by HLA-A*03:01 and C*07:01, although appropriately presented, are not immunogenic. Thus, to address an expanded patient population, phosphopeptide-targeted immunotherapies should be wary of allele-specific differences.
Antitumor activity of the investigational B7-H3 antibody-drug conjugate, vobramitamab duocarmazine, in preclinical models of neuroblastoma
Authors: Brignole Chiara , Calarco Enzo , Bensa Veronica , Giusto Elena , Perri Patrizia , Ciampi Eleonora , Corrias Maria Valeria , Astigiano Simonetta , Cilli Michele , Loo Derik , Bonvini Ezio , Pastorino Fabio , Ponzoni Mirco 
Published: September 2023

IntroductionB7-H3 is a potential target for pediatric cancers, including neuroblastoma (NB). Vobramitamab duocarmazine (also referred to as MGC018 and herein referred to as vobra duo) is an investigational duocarmycin-based antibody-drug conjugate (ADC) directed against the B7-H3 antigen. It is composed of an anti-B7-H3 humanized IgG1/kappa monoclonal antibody chemically conjugated through a cleavable valine-citrulline linker to aduocarmycin-hydroxybenzamideazaindole (vc-seco-DUBA). Vobra duo has shown preliminary clinical activity in B7-H3-expressing tumors.MethodsB7-H3 expression was evaluated by flow-cytometry in a panel of human NB cell lines. Cytotoxicity was evaluated in monolayer and in multicellular tumor spheroid (MCTS) models by the water-soluble tetrazolium salt,MTS, proliferation assay and Cell Titer Glo 3D cell viability assay, respectively. Apoptotic cell death was investigated by annexin V staining. Orthotopic, pseudometastatic, and resected mouse NB models were developed to mimic disease conditions related to primary tumor growth, metastases, and circulating tumor cells with minimal residual disease, respectively.ResultsAll human NB cell lines expressed cell surface B7-H3 in a unimodal fashion. Vobra duo was cytotoxic in a dose-dependent and time-dependent manner against all cell lines (IC50 range 5.1–53.9 ng/mL) and NB MCTS (IC50 range 17.8–364 ng/mL). Vobra duo was inactive against a murine NB cell line (NX-S2) that did not express human B7-H3; however, NX-S2 cells were killed in the presence of vobra duo when co-cultured with human B7-H3-expressing cells, demonstrating bystander activity. In orthotopic and pseudometastatic mouse models, weekly intravenous treatments with 1 mg/kg vobra duo for 3 weeks delayed tumor growth compared with animals treated with an irrelevant (anti-CD20) duocarmycin-ADC. Vobra duo treatment for 4 weeks further increased survival in both orthotopic and resected NB models. Vobra duo compared favorably to TOpotecan-TEMozolomide (TOTEM), the standard-of-care therapy for NB relapsed disease, with tumor relapse delayed or arrested by two or three repeated 4-week vobra duo treatments, respectively. Further increased survival was observed in mice treated with vobra duo in combination with TOTEM. Vobra duo treatment was not associated with body weight loss, hematological toxicity, or clinical chemistry abnormalities.ConclusionVobra duo exerts relevant antitumor activity in preclinical B7-H3-expressing NB models and represents a potential candidate for clinical translation.
Investigations of electronic, elastic, and optical properties of (Ag, Cd)-doped LaAlO3: a computational insight
Authors: Rizwan Muhammad , Moin Muhammad , Ullah Hafiz Muhammad Naeem , Anwar Abdul Waheed , Mushtaq Uzma , Mahmood Tariq 
Published: September 2023

In this study, we used density functional theory to examine how the wide band gap optoelectronic properties of pure, silver-, and cadmium-doped LaAlO3 perovskites changed. Structural, electrical, elastic, and mechanical properties were calculated using generalized gradient approximation. Silver and cadmium incorporated at Al site demonstrated a decreasing trend in the band gap. Both impurities showed the reduction in band gap from 2.98 to 0.468 eV and from 2.98 to 2.0238 eV. The density of states was examined for pristine and doped structures to understand behavioral change of LaAlO3. It was observed that p states in upper valance band and d states in lower conduction band were contributing toward the reduction of band gap. Elastic properties were computed. Elastic parameters were used to calculate Born’s stability and it is predicted that the material is stable mechanically for both pristine and doped forms. Mechanical properties were also predicted and brittle nature was found for both pristine and doped materials. Optical responses such as dielectric function, absorption, and refractive index were also predicted. The impurity inclusion in pristine structure not only reduces the bad gap but also alters the optical behavior. Absorption edge shifted toward lower energy shows a clear redshift, whereas refractive index also reduces from 2.4 to 1.9, making the material more transparent. The absorption spectrum as well as electronic band gap makes this material more useful for solar cell application as well as photocatalytic applications.
Influence of Electrodiagnostic Studies on Surgery for Carpal Tunnel Syndrome: A Retrospective Analysis of Data from a Single Urban Institution
Authors: KIMURA Hiroo , MATSUO Tomoki , SUZUKI Taku , MATSUMURA Noboru , SATO Kazuki , IWAMOTO Takuji 
Published: September 2023

Background: This study aimed to clarify the influence of preoperative electrodiagnostic (EDX) utilisation and its severity on surgically treated patients with carpal tunnel syndrome (CTS). Methods: This retrospective study analysed the data of patients who underwent CTS surgery at our facility from 2012 to 2022. Data regarding age, sex, affected side, diabetes mellitus, rheumatoid arthritis, haemodialysis and insurance type were collected, along with the following clinical information: utilisation of EDX, steroid injection, number of items of preoperative physical examination and history taking, intervals between symptom onset and the initial visit and between the initial visit and surgery, type of surgical procedure and surgery categorisation (primary or revision). EDX data (EDX severity, interval between EDX and surgery and concomitant nerve lesions) were also investigated. Univariate and multivariate analyses were conducted to assess the influence of EDX utilisation and severity on clinical parameters. Results: Of the 343 hands enrolled in our study, 304 (89%) underwent preoperative EDX assessment. EDX severity was classified as normal, mild, moderate or severe in 6 (2%), 18 (6%), 102 (34%) and 178 hands (58%), respectively. After the univariate and multivariable analyses, more items of preoperative physical examination and history taking were associated with non-EDX utilisation, whereas younger age, female sex and steroid injection were associated with milder EDX. Conclusions: Increased number of items of preoperative physical examination and history taking or steroid injection were independently associated with non-EDX utilisation or milder EDX, respectively, suggesting that when thorough clinical evaluation is conducted, hand surgeons may be less likely to request for EDX before surgery. Moreover, their treatment recommendation may be influenced by EDX severity. Level of Evidence: Level III (Diagnostic)
Persistent Hourglass Constriction in Recovered Anterior Interosseous Nerve Palsy Due to Neuralgic Amyotrophy: A Case Report
Authors: MANE Satish , DOI Kazuteru , HATTORI Yasunori , SAKAMOTO Sotetsu 
Published: September 2023

The current articles recommended the interfascicular neurolysis for anterior interosseous nerve (AIN) palsy with hourglass-like fascicular constrictions (FCs) detected by ultrasonography or surgical exploration to realign to the fascicular torsion for those who failed to recover spontaneously. We present the case report of spontaneous AIN palsy recovered after conservative treatment; however, ultrasonographic findings showed persistent FCs of AIN in the arm at the beginning, at 6 weeks, and subsequent 3-year follow-ups, even after complete clinical recovery of palsy. This finding calls into question the current notion that AIN paralysis is due to FCs and that neurolysis is the best surgical treatment when spontaneous recovery does not occur for a considerable observation period. Level of Evidence: Level V (Therapeutic)
Behavioural response of Dryophytes plicatus tadpoles to the cues of non-native rainbow trout and a native snake
Authors: Méndez-Méndez Olga , Sánchez-Sánchez Renato , Hernández-Luría Jazmín , Smith Geoffrey R. , Lemos-Espinal Julio A. 
Published: September 2023

Abstract
Non-native species have numerous and significant, often negative, effects on amphibians, but that threat may be ameliorated if the native species is able to respond behaviourally to the non-native predators. We experimentally compared the behavioural response of tadpoles of the Ridged Tree Frog, Dryophytes plicatus, to cues from non-native Rainbow Trout, Oncorhynchus mykiss, to those to a native predator, the Short-tail Alpine Garter Snake, Thamnophis scaliger. Dryophytes plicatus tadpoles did not alter activity in response to cues from O. mykiss but increased activity in the presence of cues from T. scaliger, although it is possible this increase is related, at least in part, to the order of the presentation of the cues. The activity of D. plicatus tadpoles was higher in the absence of the vegetation than in its presence when exposed to predator cues, both T. scaliger and O. mykiss, but not in the control. In conclusion, our results show D. plicatus tadpoles alter their overall activity when exposed to cues from a native predator, T. scaliger, but not the non-native O. mykiss. These results may explain, in part, why D. plicatus can co-occur with T. scaliger but not O. mykiss.
Dynamics of Religious Identity Change in the Context of Georgian Crypto-Orthodoxy
Authors: Pourtskhvanidze Zakharia , Beridze Marine , Bakuradze Lia 
Published: September 2023

Abstract
In the process of the invasion wars of Shah Abbas the First (1571–1629), the history of the emergence of two Georgian language islands in Iran (Fereydany Georgian) and Azerbaijan (Ingilo Georgian) begins. The extension of control to the areas considered the cradle of Georgian Christianity, Tao, Klarjeti, Shavsheti, and partially Javakheti, can be interpreted as a reaction of the Ottoman Empire to the Caucasus policy of Shah Abbas. Due to linguistic isolation, the third Georgian language island (Our Georgian) is formed in Turkish territory. The first period of the formation of the socio-cultural landscape of the language islands can be characterized as a parallel process of simultaneous integration and isolation of the Christian minorities in the environment of the Islamic majority. The unconscious use of Christian practices preserved in the cultural memory appears as a component of this process. The distinctive feature of Georgian Crypto-Orthodoxy is the conscious as well as unconscious use or preservation of Christian cultural components. The focus is on preserving the identity of simultaneous transformation and accommodation in relation to the environment of the new Islamic majority.
Factors associated with long-term outcomes of CD19 CAR T-cell therapy for relapsed/refractory CLL
Authors: Liang Emily C. , Albittar Aya , Huang Jennifer J. , Hirayama Alexandre V. , Kimble Erik L. , Portuguese Andrew J. , Chapuis Aude , Shadman Mazyar , Till Brian G. , Cassaday Ryan D. , Milano Filippo , Kiem Hans-Peter , Riddell Stanley R. , Turtle Cameron J. , Maloney David G. , Gauthier Jordan 
Published: September 2023

Abstract
High response rates have been reported after CD19-targeted chimeric antigen receptor–modified (CD19 CAR) T-cell therapy for relapsed/refractory (R/R) chronic lymphocytic leukemia (CLL), yet the factors associated with duration of response in this setting are poorly characterized. We analyzed long-term outcomes in 47 patients with R/R CLL and/or Richter transformation treated on our phase 1/2 clinical trial of CD19 CAR T-cell therapy with an updated median follow-up of 79.6 months. Median progression-free survival (PFS) was 8.9 months, and the 6-year PFS was 17.8%. Maximum standardized uptake value (hazard ratio [HR], 1.15; 95% confidence interval [CI], 1.07-1.23; P &lt; .001) and bulky disease (≥5 cm; HR, 2.12; 95% CI, 1.06-4.26; P = .034) before lymphodepletion were associated with shorter PFS. Day +28 complete response by positron emission tomography–computed tomography (HR, 0.13; 95% CI, 0.04-0.40; P &lt; .001), day +28 measurable residual disease (MRD) negativity by multiparameter flow cytometry (HR, 0.08; 95% CI, 0.03-0.22; P &lt; .001), day +28 MRD negativity by next-generation sequencing (HR, 0.21; 95% CI, 0.08-0.51; P &lt; .001), higher peak CD8+ CAR T-cell expansion (HR, 0.49; 95% CI; 0.36-0.68; P &lt; .001), higher peak CD4+ CAR T-cell expansion (HR, 0.47; 95% CI; 0.33-0.69; P &lt; .001), and longer CAR T-cell persistence (HR, 0.56; 95% CI, 0.44-0.72; P &lt; .001) were associated with longer PFS. The 6-year duration of response and overall survival were 26.4% and 31.2%, respectively. CD19 CAR T-cell therapy achieved durable responses with curative potential in a subset of patients with R/R CLL. This trial was registered at www.clinicaltrials.gov as #NCT01865617.
Enhancement of the therapeutic efficacy of mesenchymal stem cell-derived exosomes in osteoarthritis
Authors: Zhang Zehao , Zhao Sheng , Sun Zhaofeng , Zhai Chuanxing , Xia Jiang , Wen Caining , Zhang Yuge , Zhang Yuanmin 
Published: September 2023

AbstractOsteoarthritis (OA), a common joint disorder with articular cartilage degradation as the main pathological change, is the major source of pain and disability worldwide. Despite current treatments, the overall treatment outcome is unsatisfactory. Thus, patients with severe OA often require joint replacement surgery. In recent years, mesenchymal stem cells (MSCs) have emerged as a promising therapeutic option for preclinical and clinical palliation of OA. MSC-derived exosomes (MSC-Exos) carrying bioactive molecules of the parental cells, including non-coding RNAs (ncRNAs) and proteins, have demonstrated a significant impact on the modulation of various physiological behaviors of cells in the joint cavity, making them promising candidates for cell-free therapy for OA. This review provides a comprehensive overview of the biosynthesis and composition of MSC-Exos and their mechanisms of action in OA. We also discussed the potential of MSC-Exos as a therapeutic tool for modulating intercellular communication in OA. Additionally, we explored bioengineering approaches to enhance MSC-Exos’ therapeutic potential, which may help to overcome challenges and achieve clinically meaningful OA therapies.