bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased prevalence and stable clustering rate of HIV-1 transmitted drug resistance strains after ‘treat-all’ in a megacity of China
Authors: Zhang Dong , Han Jingwan , Li Hanping , Zheng Chenli , Liu Zhi , Sun Zixuan , Li Hao , Li Tianyi , Wang Xiaolin , Chen Lin , Yang Zhengrong , Lan Chunlin , Li Siqi , Jia Lei , Gan Yongxia , Zhong Yifan , Li Jingyun , Li Lin , Zhao Jin 
Published: June 2023

Abstract

Objectives
The ‘treat-all’ strategy was implemented in Shenzhen, China in 2016. The effect of this extensive treatment on transmitted drug resistance (TDR) of HIV is unclear.

Methods
TDR analysis was performed, based on the partial HIV-1 pol gene obtained from the newly reported HIV-1 positive cases from 2011 to 2019 in Shenzhen, China. The HIV-1 molecular transmission networks were inferred to analyse the spread of TDR. Logistic regression was used to identify the potential risk factors with TDR mutations (TDRMs) to cluster.

Results
A total of 12 320 partial pol sequences were included in this study. The prevalence of TDR was 2.95% (363/12 320), which increased from 2.57% to 3.52% after ‘treat-all’. The TDR prevalence was increased in populations with the characteristics of CRF07_BC, being single, educated to junior college level and above, MSM and male. The sensitivities of viruses to six antiretroviral drugs were decreased. The clustering rate of TDRMs remained stable, and the sequences in the three drug resistance transmission clusters (DRTCs) were mainly found during 2011–16. CRF07_BC and CRF55_01B were the factors associated with TDRMs clustering in the networks.

Conclusions
The ‘treat-all’ strategy might have contributed to a small increase in TDR, while most of the TDRMs were distributed sporadically, which implies that the ‘treat-all’ strategy is helpful for the control of TDR in high-risk populations.
A lipid scramblase TMEM41B is involved in the processing and transport of GPI-anchored proteins
Authors: Cao Shu-Ya , Liu Yi-Shi , Gao Xiao-Dong , Kinoshita Taroh , Fujita Morihisa 
Published: June 2023

Abstract
Protein modification by glycosylphosphatidylinositol (GPI) takes place in the endoplasmic reticulum (ER). GPI-anchored proteins (GPI-APs) formed in the ER are transported to the cell surface through the Golgi apparatus. During transport, the GPI-anchor structure is processed. In most cells, an acyl chain modified to the inositol of GPI is removed by a GPI-inositol deacylase, PGAP1, in the ER. Inositol-deacylated GPI-APs become sensitive to bacterial phosphatidylinositol-specific phospholipase C (PI-PLC). We previously reported that GPI-APs are partially resistant to PI-PLC when PGAP1 activity is weakened by the deletion of selenoprotein T (SELT) or cleft lip and palate transmembrane protein 1 (CLPTM1). In this study, we found that the loss of TMEM41B, an ER-localized lipid scramblase, restored PI-PLC sensitivity of GPI-APs in SELT-knockout (KO) and CLPTM1-KO cells. In TMEM41B-KO cells, the transport of GPI-APs as well as transmembrane proteins from the ER to the Golgi was delayed. Furthermore, the turnover of PGAP1, which is mediated by ER-associated degradation, was slowed in TMEM41B-KO cells. Taken together, these findings indicate that inhibition of TMEM41B-dependent lipid scrambling promotes GPI-AP processing in the ER through PGAP1 stabilization and slowed protein trafficking.
LUBAC-mediated linear ubiquitination in tissue homeostasis and disease
Authors: Sasaki Katsuhiro , Iwai Kazuhiro 
Published: June 2023

Abstract
In addition to its role in the ubiquitin–proteasome system of protein degradation, polyubiquitination is involved in the regulation of intracellular events. Depending on the type of ubiquitin–ubiquitin linkage used, polyubiquitin can assume several types of structures. The spatiotemporal dynamics of polyubiquitin involve multiple adaptor proteins and induce different downstream outputs. Linear ubiquitination, in which the N-terminal methionine on the acceptor ubiquitin serves as the site for ubiquitin–ubiquitin conjugation, is a rare and atypical type of polyubiquitin modification. The production of linear ubiquitin chains is dependent on various external inflammatory stimuli and leads to the transient activation of the downstream NF-κB signalling pathway. This in turn suppresses extrinsic programmed cell death signals and protects cells from activation-induced cell death under inflammatory conditions. Recent evidence has revealed the role of linear ubiquitination in various biological processes under both physiological and pathological conditions. This led us to propose that linear ubiquitination may be pivotal in the ‘inflammatory adaptation’ of cells, and consequently in tissue homeostasis and inflammatory disease. In this review, we focused on the physiological and pathophysiological roles of linear ubiquitination in vivo in response to a changing inflammatory microenvironment.
Inhalation Injury Severity Score on Admission Predicts Overall Survival in Burn Patients
Authors: Flinn Ashley N , Kemp Bohan Phillip M , Rauschendorfer Catherine , Le Tuan D , Rizzo Julie A 
Published: June 2023

Abstract
Inhalation injury is diagnosed in up to one-third of burn patients and is associated with increased morbidity and mortality. There are multiple scoring systems to grade inhalation injury, but no study has evaluated the ability of these scoring systems to predict outcomes of interest such as overall survival. We conducted a prospective, observational study of 99 intubated burn patients who underwent fiberoptic bronchoscopy within 24 hr of admission and graded inhalation injury using three scoring systems: abbreviated injury score (AIS), inhalation injury severity score (I-ISS), and mucosal score (MS). Agreement between scoring systems was assessed with Krippendorff’s alpha (KA). Multivariable analyses were conducted to determine if variables were associated with overall survival. At admission, median AIS, I-ISS, and MS scores were 2 for all scoring systems. Patients who died had higher overall injury burden than those who survived and had similar median admission AIS and MS scores, but higher I-ISS scores. There was strong correlation between the inhalation injury grade at admission using the three scoring systems (KA = 0.85). On regression analysis, the only scoring system independently associated with overall survival was I-ISS (score 3 compared to scores 1–2: OR 13.16, 95% CI 1.65–105.07; P = .02). Progression of injury after initial assessment may contribute to the poor correlation between admission score and overall survival for injuries graded with AIS and MS. Repeated assessment may more accurately identify patients at increased risk for mortality.
An Observational Study of Knowledge of First Aid for Burns among Parents in Indonesia
Authors: Wahyuningtyas Eka Sakti , Handayani Estrin , Wijayatri Ratna , Wardani Septi 
Published: June 2023

Abstract
Burns represent a large portion of injuries attending emergency departments each year, with children accounting for the biggest proportion. Appropriate first aid has been shown to help improve the outcome of burns and decrease the need for surgical intervention. Several studies outside of Indonesia demonstrate inadequate parental knowledge of burns first aid, but few evaluated interventions to improve knowledge. A period of data gathering from June to September 2022 was included the parents who have offspring aged between 18 and 12. This questionnaire was developed to achieve the objectives of this study and was based on others of a similar nature. A total of 102 participants were included in this study. In total, 102 parents (79.4% female [n = 81], 20.6% male [n = 21]) were questioned. Baseline knowledge was found to be poor overall; it was found that nearly 91% of parents did not know the first-aid procedures for treating pediatric burns. However, educational initiatives were effective in advancing this knowledge. When a child got burned, nearly 68% of parents knew to use cold running water, and about 70% knew to get help from a doctor. Cold running water being applied is an extremely positive sign, which can have the most beneficial effect on the healing of the injury. No other variables analyzed were shown to be statistically significant predictors of pre- or post-test scores (all P &gt; 0.05). This study concluded that educational knowledge was effective to improve the parents’ ability in performing first aid for burn care.
Successful open surgery repair of isolated right diaphragmatic rupture in 1-year-old patient at Muhimbili National Hospital: a case report and literature review
Authors: Brighton Meshack Mushobozi , Kyaruzi Victor Meza , Nhungo Charles , Mwakimako Hassan , Salim Mohamed , Khamisi Ramadhani , Mwanga Ally 
Published: June 2023

Abstract
Diaphragmatic ruptures rarely occur in isolation, a pathology in paediatric that is difficult to diagnose and can lead to serious complications if left untreated. We present a rare case of isolated right diaphragmatic rupture with liver herniation that was successfully repaired, along with a literature review. A 1-year-old female child was admitted at Emergency Department after being involved in a motor traffic crash as a passenger. Based on clinical presentation and radiological findings, we diagnosed a diaphragmatic rapture, laparotomy was performed in which we found a right isolated diaphragmatic rupture, which was repaired primarily. After re-evaluations, the patient was discharged day 16 postoperative. It is essentially important to evaluate the level of organ damage thoroughly for making a timely informed decision in management paediatric chest trauma.
Phenomic data-driven biological prediction of maize through field-based high-throughput phenotyping integration with genomic data
Authors: Adak Alper , Kang Myeongjong , Anderson Steven L , Murray Seth C , Jarquin Diego , Wong Raymond K W , Katzfuß Matthias 
Published: June 2023

Abstract
High-throughput phenotyping (HTP) has expanded the dimensionality of data in plant research; however, HTP has resulted in few novel biological discoveries to date. Field-based HTP (FHTP), using small unoccupied aerial vehicles (UAVs) equipped with imaging sensors, can be deployed routinely to monitor segregating plant population interactions with the environment under biologically meaningful conditions. Here, flowering dates and plant height, important phenological fitness traits, were collected on 520 segregating maize recombinant inbred lines (RILs) in both irrigated and drought stress trials in 2018. Using UAV phenomic, single nucleotide polymorphism (SNP) genomic, as well as combined data, flowering times were predicted using several scenarios. Untested genotypes were predicted with 0.58, 0.59, and 0.41 prediction ability for anthesis, silking, and terminal plant height, respectively, using genomic data, but prediction ability increased to 0.77, 0.76, and 0.58 when phenomic and genomic data were used together. Using the phenomic data in a genome-wide association study, a heat-related candidate gene (GRMZM2G083810; hsp18f) was discovered using temporal reflectance phenotypes belonging to flowering times (both irrigated and drought) trials where heat stress also peaked. Thus, a relationship between plants and abiotic stresses belonging to a specific time of growth was revealed only through use of temporal phenomic data. Overall, this study showed that (i) it is possible to predict complex traits using high dimensional phenomic data between different environments, and (ii) temporal phenomic data can reveal a time-dependent association between genotypes and abiotic stresses, which can help understand mechanisms to develop resilient plants.
Analytic model for off-axis GRB afterglow images – geometry measurement and implications for measuring H0
Authors: Govreen-Segal Taya , Nakar Ehud 
Published: June 2023

ABSTRACT
We present an analytic model for measuring the jet core angle (θc) and viewing angle (θobs) of off-axis gamma-ray bursts independently of the jet angular structure outside of the core. We model the images of off-axis jets, and using this model, we show that θobs and θc can be measured using any two of the three following observables: the afterglow light curve, the flux-centroid motion, and the image width. The model is calibrated using 2D relativistic hydrodynamic simulations with a broad range of jet angular structures. We study the systematic errors due to the uncertainty in the jet structure and find that when using the light curve and centroid motion to determine θobs and θc, our formulae can be accurate to a level of 5–10 per cent and 30 per cent, respectively. In light of the Hubble tension, the systematic error in cos θobs in GRBs originating in a binary compact object merger is of special interest. We find that the systematic uncertainty on the measurement of cos θobs due to the unknown jet structure is smaller than 1.5 per cent for well-observed events. A similar error is expected if the microphysical parameters evolve at a level that is not easily detected by the light curve. Our result implies that this type of systematic uncertainty will not prevent measurement of H0 to a level of 2 per cent with a sample of well-observed GW events with resolved afterglow image motion. Applying our model to the light curve and centroid motion observations of GW170817, we find $\theta _{obs}=19.2\pm 2~\deg$ (1σ) and $\theta _c=1.5-4~\deg$.
A data compression and optimal galaxy weights scheme for Dark Energy Spectroscopic Instrument and weak lensing data sets
Authors: Ruggeri Rossana , Blake Chris , DeRose Joseph , Garcia-Quintero C , Hadzhiyska B , Ishak M , Jeffrey N , Joudaki S , Krolewski Alex , Lange J U , Leauthaud A , Porredon A , Rossi G , Saulder C , Xhakaj E , Brooks D , Dhungana G , de la Macorra A , Doel P , Gontcho S Gontcho A , Kremin A , Landriau M , Miquel R , Poppett C , Prada F , Tarlé Gregory ,   (DESI Collaboration)
Published: June 2023

ABSTRACT
Combining different observational probes, such as galaxy clustering and weak lensing, is a promising technique for unveiling the physics of the Universe with upcoming dark energy experiments. The galaxy redshift sample from the Dark Energy Spectroscopic Instrument (DESI) will have a significant overlap with major ongoing imaging surveys specifically designed for weak lensing measurements: the Kilo-Degree Survey (KiDS), the Dark Energy Survey (DES), and the Hyper Suprime-Cam (HSC) survey. In this work, we analyse simulated redshift and lensing catalogues to establish a new strategy for combining high-quality cosmological imaging and spectroscopic data, in view of the first-year data assembly analysis of DESI. In a test case fitting for a reduced parameter set, we employ an optimal data compression scheme able to identify those aspects of the data that are most sensitive to cosmological information and amplify them with respect to other aspects of the data. We find this optimal compression approach is able to preserve all the information related to the growth of structures.
Accretion disc backflow in resistive MHD simulations
Authors: Mishra R , Čemeljić M , Kluźniak W 
Published: June 2023

ABSTRACT
We investigate accretion onto a central star, with the size, rotation rate, and magnetic dipole of a young stellar object, to study the flow pattern (velocity and density) of the fluid within and outside of the disc. We perform resistive magnetohydrodynamic (MHD) simulations of thin discs, varying the parameters such as the stellar rotation rate and (anomalous) coefficients of viscosity and resistivity in the disc. To provide a benchmark for the results and to compare them with known analytic results, we also perform purely hydrodynamic (HD) simulations for the same problem. Although obtained for different situations with differing inner boundary condition, the disc structure in the HD simulations closely follows the analytic solution of Kluzniak and Kita – in particular, a region of ‘mid-plane’ backflow exists in the right range of radii, depending on the viscosity parameter. In the MHD solutions, whenever the magnetic Prandtl number does not exceed a certain critical value, the mid-plane backflow exists throughout the accretion disc, extending all the way down to the foot point of the accretion funnel flow where the disc transitions to a magnetic funnel flow. For values of the magnetic Prandtl number close to the critical value the backflow and the inner disc undergo a quasi-periodic radial oscillation, otherwise the backflow is steady, as is the disc solution. From our results, supplemented by our reading of the literature, we suggest that mid-plane backflow is a real, physical, and not only numerical feature of at least some accretion discs.
Proteomics of adjacent-to-tumor samples uncovers clinically relevant biological events in hepatocellular carcinoma
Authors: Zhu Hongwen , Lin Youpei , Lu Dayun , Wang Shisheng , Liu Yuejia , Dong Liangqing , Meng Qian , Gao Jing , Wang Yuqiu , Song Nixue , Suo Yuying , Ding Li , Wang Pei , Zhang Bing , Gao Daming , Fan Jia , Gao Qiang , Zhou Hu 
Published: June 2023

ABSTRACT
Normal adjacent tissues (NATs) of hepatocellular carcinoma (HCC) differ from healthy liver tissues and their heterogeneity may contain biological information associated with disease occurrence and clinical outcome that has yet to be fully evaluated at the proteomic level. This study provides a detailed description of the heterogeneity of NATs and the differences between NATs and healthy livers and revealed that molecular features of tumor subgroups in HCC were partially reflected in their respective NATs. Proteomic data classified HCC NATs into two subtypes (Subtypes 1 and 2), and Subtype 2 was associated with poor prognosis and high-risk recurrence. The pathway and immune features of these two subtypes were characterized. Proteomic differences between the two NAT subtypes and healthy liver tissues were further investigated using data-independent acquisition mass spectrometry, revealing the early molecular alterations associated with the progression from healthy livers to NATs. This study provides a high-quality resource for HCC researchers and clinicians and may significantly expand the knowledge of tumor NATs to eventually benefit clinical practice.
Successful Treatment of Persistent Symptomatic Coronavirus Disease 19 Infection With Extended-Duration Nirmatrelvir-Ritonavir Among Outpatients With Hematologic Cancer
Authors: Liu Catherine , Yoke Leah H , Bhattacharyya Pooja , Cassaday Ryan D , Cheng Guang-Shing , Escobar Zahra Kassamali , Ghiuzeli Cristina , McCulloch Denise J , Pergam Steven A , Roychoudhury Pavitra , Tverdek Frank , Schiffer Joshua T , Ford Emily S 
Published: June 2023

Abstract
Persistent symptomatic coronavirus disease 2019 (COVID-19) is a distinct clinical entity among patients with hematologic cancer and/or profound immunosuppression. The optimal medical management is unknown. We describe 2 patients who had symptomatic COVID-19 for almost 6 months and were successfully treated in the ambulatory setting with extended courses of nirmatrelvir-ritonavir.
PUB25 and PUB26 dynamically modulate ICE1 stability via differential ubiquitination during cold stress in Arabidopsis
Authors: Wang Xi , Zhang Xiaoyan , Song Chun-Peng , Gong Zhizhong , Yang Shuhua , Ding Yanglin 
Published: June 2023

Abstract
Ubiquitination modulates protein turnover or activity depending on the number and location of attached ubiquitin (Ub) moieties. Proteins marked by a lysine 48 (K48)–linked polyubiquitin chain are usually targeted to the 26S proteasome for degradation; however, other polyubiquitin chains, such as those attached to K63, usually regulate other protein properties. Here, we show that 2 PLANT U-BOX E3 ligases, PUB25 and PUB26, facilitate both K48- and K63-linked ubiquitination of the transcriptional regulator INDUCER OF C-REPEAT BINDING FACTOR (CBF) EXPRESSION1 (ICE1) during different periods of cold stress in Arabidopsis (Arabidopsis thaliana), thus dynamically modulating ICE1 stability. Moreover, PUB25 and PUB26 attach both K48- and K63-linked Ub chains to MYB15 in response to cold stress. However, the ubiquitination patterns of ICE1 and MYB15 mediated by PUB25 and PUB26 differ, thus modulating their protein stability and abundance during different stages of cold stress. Furthermore, ICE1 interacts with and inhibits the DNA-binding activity of MYB15, resulting in an upregulation of CBF expression. This study unravels a mechanism by which PUB25 and PUB26 add different polyubiquitin chains to ICE1 and MYB15 to modulate their stability, thereby regulating the timing and degree of cold stress responses in plants.
Tracking and blocking interdependencies of cellular BRAF-MEK oncokinase activities
Authors: Fleischmann Jakob , Schwaighofer Selina , De Falco Louis , Enzler Florian , Feichtner Andreas , Kugler Valentina , Tschaikner Philipp , Huber Roland G , Stefan Eduard 
Published: June 2023

Abstract
The selective targeting of mutated kinases in cancer therapies has the potential to improve therapeutic success and thereby the survival of patients. In the case of melanoma, the constitutively active MAPK pathway is targeted by a combinatorial inhibition of BRAF and MEK activities. These MAPK pathway players may display patient-specific differences in the onco-kinase mutation spectrum, which needs to be considered for the design of more efficient personalized therapies. Here, we extend a bioluminescence-based kinase conformation biosensor (KinCon) to allow for live-cell tracking of interconnected kinase activity states. First, we show that common MEK1 patient mutations promote a structural rearrangement of the kinase to an opened and active conformation. This effect was reversible by the binding of MEK inhibitors to mutated MEK1, as shown in biosensor assays and molecular dynamics simulations. Second, we implement a novel application of the KinCon technology for tracking the simultaneous, vertical targeting of the two functionally linked kinases BRAF and MEK1. Thus, we demonstrate that, in the presence of constitutively active BRAF-V600E, specific inhibitors of both kinases are efficient in driving MEK1 into a closed, inactive conformation state. We compare current melanoma treatments and show that combinations of BRAFi and MEKi display a more pronounced structural change of the drug sensor than the respective single agents, thereby identifying synergistic effects among these drug combinations. In summary, we depict the extension of the KinCon biosensor technology to systematically validate, anticipate, and personalize tailored drug arrangements using a multiplexed setup.
Mapping moral language on US presidential primary campaigns reveals rhetorical networks of political division and unity
Authors: Hackenburg Kobi , Brady William J , Tsakiris Manos 
Published: June 2023

Abstract
During political campaigns, candidates use rhetoric to advance competing visions and assessments of their country. Research reveals that the moral language used in this rhetoric can significantly influence citizens’ political attitudes and behaviors; however, the moral language actually used in the rhetoric of elites during political campaigns remains understudied. Using a data set of every tweet (N=139,412) published by 39 US presidential candidates during the 2016 and 2020 primary elections, we extracted moral language and constructed network models illustrating how candidates’ rhetoric is semantically connected. These network models yielded two key discoveries. First, we find that party affiliation clusters can be reconstructed solely based on the moral words used in candidates’ rhetoric. Within each party, popular moral values are expressed in highly similar ways, with Democrats emphasizing careful and just treatment of individuals and Republicans emphasizing in-group loyalty and respect for social hierarchies. Second, we illustrate the ways in which outsider candidates like Donald Trump can separate themselves during primaries by using moral rhetoric that differs from their parties’ common language. Our findings demonstrate the functional use of strategic moral rhetoric in a campaign context and show that unique methods of text network analysis are broadly applicable to the study of campaigns and social movements.