bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computationally restoring the potency of a clinical antibody against Omicron
Authors: Desautels Thomas A. , Arrildt Kathryn T. , Zemla Adam T. , Lau Edmond Y. , Zhu Fangqiang , Ricci Dante , Cronin Stephanie , Zost Seth J. , Binshtein Elad , Scheaffer Suzanne M. , Dadonaite Bernadeta , Petersen Brenden K. , Engdahl Taylor B. , Chen Elaine , Handal Laura S. , Hall Lynn , Goforth John W. , Vashchenko Denis , Nguyen Sam , Weilhammer Dina R. , Lo Jacky Kai-Yin , Rubinfeld Bonnee , Saada Edwin A. , Weisenberger Tracy , Lee Tek-Hyung , Whitener Bradley , Case James B. , Ladd Alexander , Silva Mary S. , Haluska Rebecca M. , Grzesiak Emilia A. , Earnhart Christopher G. , Hopkins Svetlana , Bates Thomas W. , Thackray Larissa B. , Segelke Brent W. ,   Tri-lab COVID-19 Consortium, Lyon Emily Z. Alipio , Anderson Penelope S. , Avila-Herrera Aram , Bennett William F. , Bourguet Feliza A. , Chen Julian C. , Coleman Matthew A. , Collette Nicole M. , Davis Anastasiia , Vannest Byron D. , Fong Erika J. , Gilmore Sean , Goncalves Andre R. , Hall Sara B. , Harmon Brooke , He Wei , Hoang-Phou Steven A. , Landajuela Mikel , Laurence Ted A. , Lee Tek Hyung , Da Silva Felipe Leno , Liu Chao , Mundhenk Terrel N. , Mohagheghi Mariam V. , McIlroy Peter R. , Pham Le Thanh Mai , Sanchez Joseph C. , Sinha Anupama , Solomon Emilia A. , Watkins Nicholas , Yang Jiachen , Ye Congwang , Zhang Boya , Lillo Antonietta Maria , Sundaram Shivshankar , Bloom Jesse D. , Diamond Michael S. , Crowe James E. , Carnahan Robert H. , Faissol Daniel M. 
Published: May 2024

AbstractThe COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs1–3 and revealed how quickly viral escape can curtail effective options4,5. When the SARS-CoV-2 Omicron variant emerged in 2021, many antibody drug products lost potency, including Evusheld and its constituent, cilgavimab4–6. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign and renew the efficacy of COV2-2130 against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and subsequent variants of concern, and provides protection in vivo against the strains tested: WA1/2020, BA.1.1 and BA.5. Deep mutational scanning of tens of thousands of pseudovirus variants reveals that 2130-1-0114-112 improves broad potency without increasing escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Our computational approach does not require experimental iterations or pre-existing binding data, thus enabling rapid response strategies to address escape variants or lessen escape vulnerabilities.
Polyurethane reinforced with micro/nano waste slag as a shielding panel for photons (experimental and theoretical study)
Authors: El-Khatib Ahmed M. , Abbas Mahmoud I. , Mahmoud Mohamed E. , Fayez-Hassan Mohammed , Khalil Mamdouh H. , Abd El Aal Ahmed 
Published: May 2024

AbstractThis study not only provides an innovative technique for producing rigid polyurethane foam (RPUF) composites, but it also offers a way to reuse metallurgical solid waste. Rigid polyurethane (RPUF) composite samples have been prepared with different proportions of iron slag as additives, with a range of 0–25% mass by weight. The process of grinding iron slag microparticles into iron slag nanoparticles powder was accomplished with the use of a high-energy ball mill. The synthesized samples have been characterized using Fourier Transform Infrared Spectroscopy, and Scanning Electron Microscope. Then, their radiation shielding properties were measured by using A hyper-pure germanium detector using point sources 241Am, 133 BA, 152 EU, 137Cs, and 60Co, with an energy range of 0.059–1.408 MeV. Then using Fluka simulation code to validate the results in the energy range of photon energies of 0.0001–100 MeV. The linear attenuation coefficient, mass attenuation coefficient, mean free path, half-value layer and tenth-value layer, were calculated to determine the radiation shielding characteristics of the composite samples. The calculated values are in good agreement with the calculated values. The results of this study showed that the gamma-ray and neutron attenuation parameters of the studied polyurethane composite samples have improved. Moreover, the effect of iron slag not only increases the gamma-ray attenuation shielding properties but also enhances compressive strength and the thermal stability. Which encourages us to use polyurethane iron-slag composite foam in sandwich panel manufacturing as walls to provide protection from radiation and also heat insulation.
Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing
Authors: Utomo Condro , Tanjung Zulfikar Achmad , Aditama Redi , Pratomo Antonius Dony Madu , Buana Rika Fithri Nurani , Putra Hadi Septian Guna , Tryono Reno , Liwang Tony 
Published: May 2024

AbstractThe hemibiotrophic Basidiomycete pathogen Ganoderma boninense (Gb) is the dominant causal agent of oil palm basal stem rot disease. Here, we report a complete chromosomal genome map of Gb using a combination of short-read Illumina and long-read Pacific Biosciences (PacBio) sequencing platforms combined with chromatin conformation capture data from the Chicago and Hi-C platforms. The genome was 55.87 Mb in length and assembled to a high contiguity (N50: 304.34 kb) of 12 chromosomes built from 112 scaffolds, with a total of only 4.34 Mb (~ 7.77%) remaining unplaced. The final assemblies were evaluated for completeness of the genome by using Benchmarking Universal Single Copy Orthologs (BUSCO) v4.1.4, and based on 4464 total BUSCO polyporales group searches, the assemblies yielded 4264 (95.52%) of the conserved orthologs as complete and only a few fragmented BUSCO of 42 (0.94%) as well as a missing BUSCO of 158 (3.53%). Genome annotation predicted a total of 21,074 coding genes, with a GC content ratio of 59.2%. The genome features were analyzed with different databases, which revealed 2471 Gene Ontology/GO (11.72%), 5418 KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthologous/KO (25.71%), 13,913 Cluster of Orthologous Groups of proteins/COG (66.02%), 60 ABC transporter (0.28%), 1049 Carbohydrate-Active Enzymes/CAZy (4.98%), 4005 pathogen–host interactions/PHI (19%), and 515 fungal transcription factor/FTFD (2.44%) genes. The results obtained in this study provide deep insight for further studies in the future.
Comprehensive analysis of two hotspot codons in the TUBB4B gene and associated phenotypes
Authors: Bodenbender Jan-Philipp , Marino Valerio , Philipp Julia , Tropitzsch Anke , Kernstock Christoph , Stingl Katarina , Kempf Melanie , Haack Tobias B. , Zuleger Theresia , Mazzola Pascale , Kohl Susanne , Weisschuh Nicole , Dell’Orco Daniele , Kühlewein Laura 
Published: May 2024

AbstractOur purpose was to elucidate the genotype and ophthalmological and audiological phenotype in TUBB4B-associated inherited retinal dystrophy (IRD) and sensorineural hearing loss (SNHL), and to model the effects of all possible amino acid substitutions at the hotspot codons Arg390 and Arg391. Six patients from five families with heterozygous missense variants in TUBB4B were included in this observational study. Ophthalmological testing included best-corrected visual acuity, fundus examination, optical coherence tomography, fundus autofluorescence imaging, and full-field electroretinography (ERG). Audiological examination included pure-tone and speech audiometry in adult patients and auditory brainstem response testing in a child. Genetic testing was performed by disease gene panel analysis based on genome sequencing. The molecular consequences of the substitutions of residues 390 and 391 on TUBB4B and its interaction with α-tubulin were predicted in silico on its three-dimensional structure obtained by homology modelling. Two independent patients had amino acid exchanges at position 391 (p.(Arg391His) or p.(Arg391Cys)) of the TUBB4B protein. Both had a distinct IRD phenotype with peripheral round yellowish lesions with pigmented spots and mild or moderate SNHL, respectively. Yet the phenotype was milder with a sectorial pattern of bone spicules in one patient, likely due to a genetically confirmed mosaicism for p.(Arg391His). Three patients were heterozygous for an amino acid exchange at position 390 (p.(Arg390Gln) or p.(Arg390Trp)) and presented with another distinct retinal phenotype with well demarcated pericentral retinitis pigmentosa. All showed SNHL ranging from mild to severe. One additional patient showed a variant distinct from codon 390 or 391 (p.(Tyr310His)), and presented with congenital profound hearing loss and reduced responses in ERG. Variants at codon positions 390 and 391 were predicted to decrease the structural stability of TUBB4B and its complex with α-tubulin, as well as the complex affinity. In conclusion, the twofold larger reduction in heterodimer affinity exhibited by Arg391 substitutions suggested an association with the more severe retinal phenotype, compared to the substitution at Arg390.
Electrophysiological correlates of sustained conscious perception
Authors: Hense Annika , Peters Antje , Bruchmann Maximilian , Dellert Torge , Straube Thomas 
Published: May 2024

AbstractPrevious research on the neural correlates of consciousness (NCC) in visual perception revealed an early event-related potential (ERP), the visual awareness negativity (VAN), to be associated with stimulus awareness. However, due to the use of brief stimulus presentations in previous studies, it remains unclear whether awareness-related negativities represent a transient onset-related response or correspond to the duration of a conscious percept. Studies are required that allow prolonged stimulus presentation under aware and unaware conditions. The present ERP study aimed to tackle this challenge by using a novel stimulation design. Male and female human participants (n = 62) performed a visual task while task-irrelevant line stimuli were presented in the background for either 500 or 1000 ms. The line stimuli sometimes contained a face, which needed so-called visual one-shot learning to be seen. Half of the participants were informed about the presence of the face, resulting in faces being perceived by the informed but not by the uninformed participants. Comparing ERPs between the informed and uninformed group revealed an enhanced negativity over occipitotemporal electrodes that persisted for the entire duration of stimulus presentation. Our results suggest that sustained visual awareness negativities (SVAN) are associated with the duration of stimulus presentation.
Infektionen und Multiple Sklerose
Authors: Heidler Felicita , Bopp Tobias , Schwab Matthias , Hoffmann FrankA , Schild Hansjörg , Kannler Martina , Pletz Mathias , Zettl Uwe K. 
Published: May 2024

ZusammenfassungIn der Studienliteratur nehmen die Ursachen, Bedingungen und Folgen von
Infektionen bei Patienten mit einer Multiplen Sklerose (MS) nicht den Platz ein,
der ihnen von der Alltagsrelevanz her zustünde. Gerade Harnwegsinfekte und vor
allem Pneumonien tragen erheblich zu Krankenhauseinweisungen, Morbidität und
Mortalität bei. In dieser Übersicht werden die aktuellen Erkenntnisse zu den
Infektionskrankheiten einschließlich SARS-CoV-2 bei der MS zusammengefasst.
Dabei geht es um drei Fragestellungen: Beeinflussen Infektionen das MS-Risiko?
Wirken sich Infektionen auf die Krankheitsaktivität bei der MS aus? Welche
Effekte haben die verschiedenen immunmodulatorischen MS-Therapien auf das Risiko
und den Verlauf von Infektionskrankheiten? Um die Beratung und Versorgung der
MS-Patienten zu verbessern, werden die Studienlage und aktuelle Empfehlungen
überprüft und erörtert, was im Behandlungsalltag zu beachten ist.
Oridonin Attenuates Diabetes‑induced Renal Fibrosis via the
Inhibition of TXNIP/NLRP3 and NF‑κB Pathways by Activating PPARγ in
Rats
Authors: Huang Gengzhen , Zhang Yaodan , Zhang Yingying , Zhou Xiaotao , Xu Yuan , Wei Huiting , Chen Xian , Ma Yuerong 
Published: May 2024

Abstract
Introduction Oridonin possesses remarkable anti-inflammatory,
immunoregulatory properties. However, the renoprotective effects of oridonin and
the underlying molecular mechanisms in diabetic nephropathy (DN). We
hypothesized that oridonin could ameliorate diabetes‑induced renal fibrosis.
Methods Streptozocin (STZ)-induced diabetic rats were provided with a
high-fat diet to establish a type 2 diabetes mellitus (T2DM) animal model, and
then treated with Oridonin (10, 20 mg/kg/day) for two weeks. Kidney function and
renal fibrosis were assessed. High glucose-induced human renal proximal tubule
epithelial cells (HK-2) were also treated with oridonin. The expression of
inflammatory factors and fibrotic markers were analyzed.
Results Oridonin treatment preserved kidney function and markedly limited
the renal fibrosis size in diabetic rats. The renal fibrotic markers were
inhibited in the oridonin 10 mg/kg/day and 20 mg/kg/day groups compared to the
T2DM group. The expression of thioredoxin-interacting proteins/ nod-like
receptor protein-3 (TXNIP/NLRP3) and nuclear factor (NF)‑κB pathway decreased,
while that of peroxisome proliferator-activated receptor-gamma (PPARγ) increased
in the oridonin treatment group compared to the non-treated group. In vitro,
PPARγ intervention could significantly regulate the effect of oridonin on the
high glucose-induced inflammatory changes in HK-2 cells.
Conclusion Oridonin reduces renal fibrosis and preserves kidney function
via the inhibition of TXNIP/NLRP3 and NF‑κB pathways by activating PPARγ in rat
T2DM model, which indicates potential effect of oridonin in the treatment of
DN.
Spectroscopic analysis of the sum-frequency response of the carbon–hydrogen stretching modes in collagen type I
Authors: Luna Palacios Yryx Y. , Khandani Salile , Garcia Evan P. , Chen Anabel , Wang Siyang , Roy Khokan , Knez David , Kim Do A. , Rocha-Mendoza Israel , Potma Eric O. 
Published: May 2024

We studied the origin of the vibrational signatures in the sum-frequency generation (SFG) spectrum of fibrillar collagen type I in the carbon–hydrogen stretching regime. For this purpose, we developed an all-reflective, laser-scanning SFG microscope with minimum chromatic aberrations and excellent retention of the polarization state of the incident beams. We performed detailed SFG measurements of aligned collagen fibers obtained from rat tail tendon, enabling the characterization of the magnitude and polarization-orientation dependence of individual tensor elements Xijk2 of collagen’s nonlinear susceptibility. Using the three-dimensional atomic positions derived from published crystallographic data of collagen type I, we simulated its Xijk2 elements for the methylene stretching vibration and compared the predicted response with the experimental results. Our analysis revealed that the carbon–hydrogen stretching range of the SFG spectrum is dominated by symmetric stretching modes of methylene bridge groups on the pyrrolidine rings of the proline and hydroxyproline residues, giving rise to a dominant peak near 2942 cm−1 and a shoulder at 2917 cm−1. Weak asymmetric stretches of the methylene bridge group of glycine are observed in the region near 2870 cm−1, whereas asymmetric CH2-stretching modes on the pyrrolidine rings are found in the 2980 to 3030 cm−1 range. These findings help predict the protein’s nonlinear optical properties from its crystal structure, thus establishing a connection between the protein structure and SFG spectroscopic measurements.
Mid-infrared Fine Structure Lines from the Galactic Warm Ionized Medium
Authors: Kulkarni S. R. , Beichman Charles , Ressler Michael E. 
Published: May 2024

Abstract
The Warm Ionized Medium (WIM) hosts most of the ionized gas in the Galaxy and occupies perhaps a quarter of the volume of the Galactic disk. Decoding the spectrum of the Galactic diffuse ionizing field is of fundamental interest. This can be done via direct measurements of ionization fractions of various elements. Based on current physical models for the WIM we predicted that mid-IR fine structure lines of Ne, Ar and S would be within the grasp of the Mid-Infrared Imager-Medium Resolution Spectrometer (MIRI-MRS), an Integral Field Unit (IFU) spectrograph, aboard the James Webb Space Telescope (JWST). Motivated thus we analyzed a pair of commissioning data sets and detected [Ne ii] 12.81 μm, [S iii] 18.71 μm and possibly [S iv] 10.51 μm. The inferred emission measure for these detections is about 10 cm−6 pc, typical of the WIM. These detections are broadly consistent with expectations of physical models for the WIM. The current detections are limited by uncorrected fringing (and to a lesser extent by baseline variations). In due course, we expect, as with other IFUs, the calibration pipeline to deliver photon-noise-limited spectra. The detections reported here bode well for the study of the WIM. Along most lines-of-sight hour-long MIRI-MRS observations should detect line emission from the WIM. When combined with optical observations by modern IFUs with high spectral resolution on large ground-based telescopes, the ionization fraction and temperature of neon and sulfur can be robustly inferred. Separately, the ionization of helium in the WIM can be probed by NIRspec. Finally, joint JWST and optical IFU studies will open up a new cottage industry of studying the WIM on arcsecond scales.
Introduction
Authors: Hebbar N. Nandini 
Published: May 2024

Abstract
The introductory chapter examines how the immense social value placed on technical education as a viable route to a good life, respectable middle-class identity, and high status have contributed to a specific kind of subject-making on engineering campuses across Tamil Nadu. While enforcing a performativity of the acceptable in the social realm, the institutional structure also propagates a pedagogy that is uncritical and mechanically derived; a pedagogy that emphasizes application over criticism, and structure over individual. Though students are not simply ‘interpellated’ by this pedagogy and disciplinary framework in an Althusserian manner, it does have a role to play in crafting a distinct subjectivity and sense of self-worth. Even as students negotiate these institutional constraints, it has become an integral part of college life and the ways in which ‘youth’ is experienced.
Identification of 2 Novel Subtypes of Hepatitis C Virus Genotype 8 and a Potential New Genotype Successfully Treated With Direct Acting Antivirals
Authors: Mbisa Jean L , Lapp Zena , Bibby David F , Phillips Laura T , Manso Carmen F , Packer Simon , Simmons Ruth , Harris Kathryn , Mohan Jaiganesh , Chinnappan Lalitha , Leitner Thomas , Bradshaw Daniel 
Published: May 2024

Abstract

Background
Hepatitis C virus (HCV) has high genetic diversity and is classified into 8 genotypes and &gt;90 subtypes, with some endemic to specific world regions. This could compromise direct-acting antiviral efficacy and global HCV elimination.

Methods
We characterized HCV subtypes “rare” in the United Kingdom (non-1a/1b/2b/3a/4d) by means of whole-genome sequencing via a national surveillance program. Genetic analyses to determine the genotype of samples with unresolved genotypes were undertaken by comparison with International Committee on Taxonomy of Viruses HCV reference sequences.

Results
Two HCV variants were characterized as being closely related to the recently identified genotype (GT) 8, with &gt;85% pairwise genetic distance similarity to GT8 sequences and within the typical intersubtype genetic distance range. The individuals infected by the variants were UK residents originally from Pakistan and India. In contrast, a third variant was only confidently identified to be more similar to GT6 compared with other genotypes across 6% of the genome and was isolated from a UK resident originally from Guyana. All 3 were cured with pangenotypic direct-acting antivirals (sofosbuvir-velpatasvir or glecaprevir-pibrentasvir) despite the presence of resistance polymorphisms in NS3 (80K/168E), NS5A (28V/30S/62L/92S/93S) and NS5B (159F).

Conclusions
This study expands our knowledge of HCV diversity by identifying 2 new GT8 subtypes and potentially a new genotype.
Prevalence of polymyxin-resistant bacterial strains in India: a systematic review and meta-analysis
Authors: Dwibedy Sambit K , Padhy Indira , Panda Aditya K , Mohapatra Saswat S 
Published: May 2024

AbstractIntroductionPolymyxins, the cationic lipopeptide antibiotics, are the last line of therapeutics against the MDR Gram-negative bacterial (GNB) pathogens. Unfortunately, the rising cases of polymyxin-resistant strains from across the globe have adversely impacted their utility. While the molecular mechanisms responsible for developing polymyxin resistance (PolR) are largely understood, the prevalence of PolR strains in India has not been investigated systematically. The current study was undertaken to primarily determine the prevalence of PolR strains in India. Moreover, the extent of the spread of mobile colistin resistance (mcr) genes among the GNB strains in India was also determined.MethodA systematic search for articles using the relevant inclusion and exclusion criteria was performed in the applicable databases for the period January 2015 to December 2023. The included 41 studies were subjected to a meta-analysis using the Comprehensive Meta-Analysis software (V4.0). Publication biases were assessed using funnel plots and Egger’s regression analysis.ResultConsidering a total of 41 studies including 24 589 bacterial isolates the present meta-analysis found the rate of PolR bacteria in India to be at 15.0% (95% CI: 11.2 to 19.8). Among the Indian States, Tamil Nadu topped with the highest prevalence of PolR at 28.3%. Investigating the contribution of the mcr genes, it was observed that among the PolR strains, 8.4% (95% CI: 4.8 to 14.3) were mcr positive.ConclusionThe study determined the prevalence of PolR strains in India at 15.0%, which is higher than that of the global average at 10%. The study also determined that 8.4% of the PolR strains carried the mcr genes. The mcr-positive strains reported from India could be an underestimation of the actual numbers due to the non-inclusion of mcr screening in many previous studies. This study provides insight into the state of the PolR situation in India, which may be useful to develop a monitoring strategy to contain the spread of such strains and preserve the efficacy of the polymyxins.