bluuebunny/crossref_metadata_2025 huggingface dataset:
CLINICAL TRIAL FOR LEVOFLOXACIN VERSUS AMOXYCILLIN/CLAVULANIC ACID COMBINED WITH AZITHROMYCIN IN TREATMENT OF COMMUNITY ACQUIRED PNEUMONIA
Authors: Musungu Vincent , Onguru Daniel , Onyango Patrick
Published: July 2023

Background

Community acquired pneumonia (CAP) is an important cause of mortality and morbidity worldwide. Early initiation of antibiotics is highly recommended. In most CAP cases, multiple drug options are increasingly becoming available, but there is often a lack of evidence that allows for direct comparison of the efficacy of one drug versus another. The purpose of this study was to investigate the effectiveness of antibiotics so as to rationalize outpatient treatment of community acquired pneumonia among patients with previous antibiotic exposure.

Aim

The main objective was to compare treatment outcomes using oral levofloxacin alone and combined azithromycin and amoxicillin/Clavulanic acid in outpatient treatment of Community acquired pneumonia.

Methods

This study was a prospective longitudinal design. Patients diagnosed to have CAP were put into first and second treatment groups. Community acquired pneumonia was diagnosed according to America Thoracic Society criteria. Sample size of 76 was arrived at by Cochran’s formular. Variation in white blood cell counts at baseline and after treatment in the two treatment groups was analysed using ANOVA whereas differences in treatment outcome was analysed using the independent t-test.

Results

The findings of this study suggest that combination of azithromycin and amoxycillin/clavulanic acid was associated with statistically significant faster resolution of chest pains and cough (mean 1.7 and 3.14 days respectively) compared to levofloxacin group (mean 2.21 and 3.71 days respectively) in patients who had community acquired pneumonia (p=0.009). However, in the two treatment groups, there was no difference in the meantime to fever resolution, time to crackles subsidence, resolution of difficulty in breathing and change in white blood cell count.

Conclusions

Based on the quantitative analysis and methodology used by the current study, it can be concluded that although both treatment groups demonstrated similar effectiveness, combination of amoxicillin/clavulanic acid and azithromycin showed a modest superiority in relation to rate of symptom resolution and change in white blood cell count.
Telemedicine adoption in Ecuador: an assessment of physician perceptions and knowledge towards its benefits and limitation
Authors: Cherrez-Ojeda Ivan , Vanegas Emanuel , Felix Miguel , Bajaña María José Farfán , Alvarado-Villa Geovanny , Mautong Hans , Espinoza Fernando , Sarfraz Zouina , Sarfraz Azza , Robles-Velasco Karla , Michel Jack , Lahmar Abdelilah , Zimmermann Luc J. I. , Gavilanes Antonio WD
Published: July 2023

Telemedicine is a growing field with the potential to improve healthcare delivery, however it is important for a proper implementation to understand how physicians perceive the benefits and limitations related to their use. With this study our aim is to assess the perceptions and knowledge of telemedicine among a sample of Ecuadorian healthcare providers. We conducted a cross-sectional online survey-based study where participants answered a 12-item survey assessing their knowledge and perceptions towards telemedicine. Demographic variables were analyzed applying descriptive statistics, and a chi-square goodness of fit test was used to assess the observed frequencies of each of the survey’s queries. In total, 382 participants completed the survey with an average age of 51.3 years (SD, 11.4). Around half of participants expressed to be lowly to very lowly familiarized with telemedicine technology (χ2(4) = 88.497, p = .000). Most of them considered to a high extent that telemedicine is effective in reducing costs of patient care in hospitals (32.5%; n=124; χ2(4) = 78.812, p = .000). Finally, 8 out 10 participants expressed that a framework should be created to prevent breaches of data confidentiality when using telemedicine (χ2(4) = 250.749, p = .000). In this study we found a considerable proportion of physicians reporting low familiarization with telemedicine despite being aware of the benefits it can bring to patient care. Breaches of data confidentially and the potential for malpractice were cited as main concerns in need of a framework to prevent them. Future studies are needed to address the perceived barriers of technology to ensure a safe and efficient use of telemedicine in the healthcare setting.
COVID-19 vaccine information, misinformation, and vaccine uptake in Malawi
Authors: Songo John , Whitehead Hannah S. , Phiri Khumbo , Kalande Pericles , Lungu Eric , Phiri Sam , van Oosterhout Joep J. , Moses Agnes , Hoffman Risa M. , Moucheraud Corrina
Published: July 2023

Background

COVID-19 vaccine information – including source, content, and tone – may be an important determinant of vaccination, but this dynamic is not well-understood in low-income countries where COVID-19 vaccine uptake remains low. We assessed the COVID-19 vaccine information environment in Malawi, and its correlation with vaccine uptake.

Methods

A survey was administered among 895 adult (≥18 years) clients at 32 Malawian health facilities in mid-2022. Respondents reported their COVID-19 vaccination history, exposure to information about the COVID-19 vaccine from different sources and its tone (positive, negative, or neutral/factual), and whether they had heard of and believed in ten COVID-19 and COVID-19 vaccine conspiracy theories. We described the COVID-19 vaccine information environment in Malawi and used logistic regression analyses to assess the association of exposure to information sources and conspiracy theories with uptake of the COVID-19 vaccine.

Results

Respondents had received information about the COVID-19 vaccine most commonly from friends and neighbors, healthcare workers, and radio (each reported by >90%). Men, urban residents, and respondents with a higher education level were exposed to more COVID-19 vaccine information sources. COVID-19 vaccine uptake was positively associated with exposure to a greater number of COVID-19 vaccine information sources (aOR 1.09, 95% CI 1.03-1.15), and more positive information (aOR 4.33, 95% CI 2.17-8.64) – and was negatively associated with believing COVID-19 vaccine conspiracy theories to be true (OR 0.76, 95% CI 0.68-0.87).

Conclusions

Malawian adults were exposed to a variety of COVID-19 vaccine information sources, with less access to information among women, rural residents, and people with lower educational attainment. Exposure to misinformation was common, though infrequently believed. Vaccination was associated with exposure to high number of COVID-19 vaccine information sources, exposure to positive vaccine information and endorsing fewer conspiracy theories. Vaccination programs should disseminate communication with positive messaging, through multiple information sources, prioritizing the less exposed groups we identified.
Accuracy of clinical risk factor-based models as a screening test for detecting gestational diabetes mellitus in a low-resource setting
Authors: Senbanjo Olayinka Comfort , Akinlusi Fatimat Motunrayo , Rabiu Kabiru Afolarin
Published: July 2023

Current World Health Organization guidelines recommend fasting 2-hour tests for all pregnant women, a strategy that is burdensome for patients as well as time and labor-intensive for health systems. There have been suggestions for the use of clinical risk factors-based models as alternatives. These have not been widely tested especially in low-resource countries. We aimed to determine the prevalence of GDM and the accuracy of clinical risk factor-based models as screening tools for detecting GDM.

This was a prospective cohort study of consenting 400 pregnant women receiving antenatal care at a tertiary health facility in Lagos, Nigeria. All the study subjects were assessed for the risk of GDM using three different clinical risk-based models. They also had universal screening for GDM at 24–28 weeks gestational age using the gold standard 2-hour 75g Oral Glucose Tolerance Test (OGTT). Statistical analysis was done using the statistical package for social science version 24. The Receiver Operating Curve (ROC) was used to determine the accuracy of the risk factor-based models.

The mean age of the subjects was 31.0±5.3 years. A total of 76 subjects met the IADPSG/WHO 2013 criteria giving a prevalence of 19.0%. According to the clinical risk scores by Nayloret al, Caliskanet aland Phaloprakarnet al,340 (85%), 269 (67.3%) and 375 (93.8%) participants respectively had a risk score positive for GDM. If the study participants were selectively screened based on these models, between 71.1-96.1% of the women with GDM would have been identified and 6.3-32.8% of the women would not have performed the diagnostic test. The models had areas under the ROC that ranges between 51.6-52.9%.

Conclusions:The prevalence of GDM is high and the clinical risk factor-based prediction models tested in this study could be used to stratify low-risk women out of diagnostic tests.
TRENDS, IN-HOSPITAL OUTCOMES, AND INDEPENDENT PREDICTORS OF ACUTE KIDNEY INJURY IN PATIENTS ADMITTED FOR MYOCARDIAL INFARCTION WITH PERCUTANEOUS CORONARY INTERVENTION: An insight from the National Inpatient Sample Database
Authors: Antia Akanimo , Ubokudom Daniel , Adabale Olanrewaju , Okorare Ovie , Daniel Emmanuel , Evbayekha Endurance , Onuegbu Chinwendu Angel , Ong Kenneth
Published: July 2023

Background

Acute kidney injury (AKI) is an important risk factor associated with adverse outcomes in cardiovascular illnesses, more importantly, myocardial infarction (MI). This study describes the Trends, in-hospital outcomes, and independent predictors of Acute Kidney Injury (AKI) in patients admitted for Myocardial infarction with Percutaneous Coronary Intervention (PCI).

Methods

This retrospective study used patient records from the 2016-2020 National In-patient Database (NIS). We identified patients who were admitted for the management of an MI who had a PCI procedure and an AKI and evaluated their associated socio-demographic and comorbid factors using International Classification of Diseases-10 (ICD-10) codes. The chi-square test was used to compare baseline characteristics between our populations with and without AKI and outcomes and multivariate logistic regression to identify independent predictors of AKI.

Results

There were 1,551,630 patients admitted for an MI and PCI, with 15% having an AKI. We observed that our population with AKI were older on admission and were more likely to be whites than blacks. A higher percentage were males. Our subpopulation was likely to have heart failure, atrial fibrillation, coronary artery disease, obesity, CKD and Charlson comorbidity index ≥ 3. A diagnosis of AKI was associated with higher in-hospital mortality rates [adjusted odds ratio (aOR): 2.84, CI: 2.7–3.02, p<0.001], longer mean length of stay (LOS) and higher hospital costs. We noted an increasing trend in the percentage of patients who had an AKI, from about 13.5% in 2016 to 16.5% in 2020.

Conclusion

Acute Kidney Injury is strongly associated with worse hospital outcomes in patients admitted for MI and PCI, with higher mortality rates, a longer mean length of stay, and a higher hospitalization cost. A more concise look at preventive measures is recommended to minimize these outcomes.
Comparative Assessment of Myocardial Work Performance during Spontaneous Rhythm, His Bundle Pacing, and Left Bundle Branch Area Pacing: Insights from the EMPATHY Study
Authors: Azzolini Giorgia , Bianchi Nicola , Vitali Francesco , Malagù Michele , Balla Cristina , Raffele Martina De , Bertini Matteo
Published: July 2023

Background

Physiological pacing has gained significant interest due to its potential to achieve optimal hemodynamic response. This study aimed to assess left ventricular performance in terms of electrical parameters, specifically QRS duration, and mechanical performance, evaluated as myocardial work. We compared His Bundle Pacing (HBP) and Left Bundle Branch Area Pacing (LBBAP) to evaluate their effects.

Methods

Twenty-four patients with class I or IIa indications for pacing were enrolled in the study, with 12 patients undergoing HBP implantation and another 12 patients undergoing LBBAP implantation. A comprehensive analysis of myocardial work was conducted.

Results

Our findings indicate that there were no major differences in terms of spontaneous and HBP activation in myocardial work, except for global wasted work (217 mmHg% vs. 283 mmHg%; p 0.016) and global work efficiency (87 mmHg% vs. 82 mmHg%; p 0.049). There were no significant differences observed in myocardial work between spontaneous activation and LBBAP. Similarly, no significant differences in myocardial work were found between HBP and LBBAP.

Conclusions

Both pacing modalities provide physiological ventricular activation without significant differences when compared to each other. Moreover, there were no significant differences in QRS duration between HBP and LBBAP.

However, LBBAP demonstrated advantages in terms of feasibility, as it achieved better lead electrical parameters compared to HBP (threshold@0.4 ms 0.6 V vs. 1 V; p=0.045. Sensing 9.4 mV vs. 2.4 mV; p<0.001). Additionally, LBBAP required less fluoroscopy time (6 min vs. 13 min; p=0.010) and procedural time (81 min vs. 125 min; p=0.004) compared to HBP.

Clinical Perspective

What is Known

His Bundle Pacing (HBP) and Left Bundle Branch Area Pacing (LBBAP) have been recognized as more physiological alternatives to traditional right ventricular pacing. LBBAP has shown greater feasibility compared to HBP, although direct comparison data between the myocardial work in HBP and LBBAP are limited.

What the Study Adds

Our study contributes to the existing knowledge by demonstrating that both HBP and LBBAP provide physiological ventricular activation, with no significant differences observed between the two pacing modalities in terms of myocardial work and QRS duration. However, LBBAP showcased advantages such as reduced need for fluoroscopy, shorter procedural time, and improved electrical parameters. These findings further support the potential of LBBAP as a favorable pacing option.

Graphical abstract
Left common trunkus pulmonary veins have genetic background and poorer rhythm outcome after paroxysmal atrial fibrillation catheter ablation
Authors: Choi Sung Hwa , Kim Tae-Hoon , Hong Myunghee , Kwon Oh-Seok , Kim Daehoon , Park Je-Wook , Yu Hee Tae , Uhm Jae-Sun , Joung Boyoung , Lee Moon-Hyoung , Hwang Chun , Pak Hui-Nam
Published: July 2023

Background

The genetic traits of pulmonary vein (PV) variants and rhythm outcomes after atrial fibrillation (AF) catheter ablation (AFCA) remain unclear. We explored the genetic and clinical characteristics and long-term rhythm outcomes of patients with AF and left common trunkus (LCT)-PVs or accessory PVs.

Methods

We included 2,829 patients with AF (74.0% men, age 59.1±10.7 years, 66.3% paroxysmal AF) and available genome-wide association study, cardiac computed tomography, and protocol-based regular rhythm follow-up results from the Yonsei AF ablation cohort database. We examined 1,223 single nucleotide polymorphisms in 12 genetic loci associated with AF and long-term rhythm outcomes after AFCA.

Results

We found LCT-PVs in 91(3.2%) and accessory PVs in 189(6.7%) patients. Rs9871453 (SCN10A) and rs1979409 (NEO1) were significantly associated with LCT-PV occurrence, and polygenic risk score (PRS) differed significantly between patients with LCT-PVs (p=1.64e-05) and normal PVs, but not those with accessory PVs (p=0.939). Patients with LCT-PVs had a higher proportion of the female sex(p=0.046) and CHA2DS2VASc score (p=0.026). After follow-up for 39.7±4.7 months, patients with LCT-PVs exhibited significantly greater LCT anterior wall thicknesses (p<0.001) and higher recurrence rate than those with normal PVs, particularly patients with paroxysmal AF (log-rank, p=0.042). LCT-PVs were independently associated with AF recurrence after AFCA (hazard ratio[HR], 2.26 [1.01–4.42]; p=0.046). Patients with LCT-PVs and higher PRSs had a higher risk of recurrent AF (adjusted HR 1.78, 95% CI 1.10–2.88, p=0.019).

Conclusions

Patients with LCT-PVs have a significant genetic background. Post-AFCA recurrence rate was significantly higher in patients with LCT-PVs and higher PRSs, particularly in those with paroxysmal AF.

Clinical Perspective

What Is New?

This study identifies specific genetic variants associated with the occurrence of LCT-PVs in AF patients undergoing catheter ablation.

Higher AF recurrence rates were observed in LCT-PV patients, particularly those with paroxysmal AF. High-genetic risk LCT-PV patients exhibited increased AF recurrence and a thicker anterior wall of the left pulmonary vein compared to normal PV patients.

What Are the Clinical Implications?

The findings enhance our understanding of the genetic basis of AF and its anatomical manifestations, enabling personalized treatment approaches.

Further research is needed to identify additional genetic variants associated with LCT-PV and to understand the recurrence of AF when using methods other than catheter ablation.
Dynamicity of brain network organization and their community architecture as characterizing features for classification of common mental disorders from the whole-brain connectome
Authors: Sastry Nisha Chetana , Banerjee Arpan
Published: July 2023

The urgency of addressing common mental disorders (bipolar disorder, ADHD, and schizophrenia) arises from their significant societal impact. Developing strategies to support psychiatrists is crucial. Previous studies focused on the relationship between these disorders and changes in the resting-state functional connectome’s modularity, often using static functional connectivity (sFC) estimation. However, understanding the dynamic reconfiguration of resting-state brain networks with rich temporal structure is essential for comprehending neural activity and addressing mental health disorders. This study proposes an unsupervised approach combining spatial and temporal characterization of brain networks to classify common mental disorders using fMRI timeseries data from two cohorts (N=408 participants). We employ the weighted stochastic block model to uncover mesoscale community architecture differences, providing insights into neural organization. Our approach overcomes sFC limitations and biases in community detection algorithms by modelling the functional connectome’s temporal dynamics as a landscape, quantifying temporal stability at whole-brain and network levels. Findings reveal individuals with schizophrenia exhibit less assortative community structure and participate in multiple motif classes, indicating less specialized neural organization. Patients with schizophrenia and ADHD demonstrate significantly reduced temporal stability compared to healthy controls. This study offers insights into functional connectivity (FC) patterns’ spatiotemporal organization and their alterations in common mental disorders, highlighting the potential of temporal stability as a biomarker.
PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity and Antibody Developability
Authors: Waibl Franz , Pomarici Nancy D. , Hoerschinger Valentin J. , Loeffler Johannes R. , Deane Charlotte M. , Georges Guy , Kettenberger Hubert , Fernández-Quintero Monica L. , Liedl Klaus R.
Published: July 2023

The electrostatic properties of proteins arise from the number and distribution of polar and charged residues. Due to their long-ranged nature, electrostatic interactions in proteins play a critical role in numerous processes, such as molecular recognition, protein solubility, viscosity, and antibody developability. Thus, characterizing and quantifying electrostatic properties of a protein is a pre-requisite for understanding these processes. Here, we present PEP-Patch, a tool to visualize and quantify the electrostatic potential on the protein surface and showcase its applicability to elucidate protease substrate specificity, antibody-antigen recognition and predict heparin column retention times of antibodies as an indicator of pharmacokinetics.
Metabolomics and Microbiomics Insights into the Differential Surface Fouling of Brown Algae
Authors: Oppong-Danquah Ernest , Blümel Martina , Tasdemir Deniz
Published: July 2023

Marine macroalgae (seaweeds) are key components of marine ecosystems with vital roles in costal habitats. As they release dissolved organic matter and other molecules, seaweeds are under strong settlement pressure by micro- and macro-epibionts. Uncontrolled epibiosis causes surface fouling with detrimental effects on the health and well-being of the organism. Seaweeds control surface epibionts directly by releasing antifouling and antimicrobial metabolites onto their surfaces, and indirectly by recruiting beneficial microorganisms that produce antimicrobial/antifouling metabolites. Three species of the brown algal genusFucus, F. vesiculosus(FV), F. serratus(FS) andF. distichussubsp.evanescens(FE) form theFucusbelt habitat in the Kiel Fjord, Germany. They often co-occur in the same spot but their blades are fouled differently; we observed FE to be the least fouled, and FV to be the most fouled species. This study was designed to investigate the potential factors underlying different fouling intensities on the surfaces of the three co-occurringFucusspp. Their surface metabolomes were analysed by comparative untargeted UPLC-MS/MS based metabolomics to identify marker metabolites influencing the surface fouling. The epiphytic microbial communities of theFucusspp. were also comparatively characterized by high-throughput amplicon sequencing to identify the differences in the surface microbiome of the algae. By employing these omics methods, integrated with multivariate analyses, we identified discriminant metabolites and microbial taxa associated with FE surface, including antimicrobial polar lipids, the fungal generaMucor,Alternaria, and bacterial genusYoonia-Loktanella. These taxa have been previously reported to produce antimicrobial and antifouling compounds, suggesting their potential involvement in the fouling resistance (least fouled) observed on the FE surface relative to the co-occurring algae FS and FV. These findings shed light on the surface metabolome and microbiome ofFucusspp. and their influence in different fouling intensities and also have implications for the conservation of coastal habitats.
Increased beta2-adrenergic signaling is a targetable stimulus essential for bone healing by promoting callus neovascularization
Authors: Jahn Denise , Knapstein Paul Richard , Otto Ellen , Köhli Paul , Sevecke Jan , Graef Frank , Graffmann Christine , Fuchs Melanie , Jiang Shan , Rickert Mayla , Erdmann Cordula , Appelt Jessika , Revend Lawik , Küttner Quin , Witte Jason , Rahmani Adibeh , Duda Georg , Xie Weixin , Donat Antonia , Schinke Thorsten , Ivanov Andranik , Tchouto Mireille Ngokingha , Beule Dieter , Frosch Karl-Heinz , Baranowsky Anke , Tsitsilonis Serafeim , Keller Johannes
Published: July 2023

Traumatic brain injury (TBI) is associated with a hyperadrenergic state and paradoxically causes systemic bone loss while accelerating fracture healing. Here, we identify the beta2-adrenergic receptor (Adrb2) as a central mediator of these skeletal manifestations. While the negative effects of TBI on the unfractured skeleton can be explained by the established impact of Adrb2 signaling on bone formation, Adrb2 promotes neovascularization of the fracture callus under conditions of high sympathetic tone, including TBI and advanced age. Mechanistically, norepinephrine stimulates the expression of Vegfa and Cgrp primarily in periosteal cells via Adrb2, both of which synergistically promote the formation of osteogenic type-H vessels in the fracture callus. Accordingly, the beneficial effect of TBI on bone repair is abolished in mice lacking Adrb2 or Cgrp, and aged Adrb2-deficient mice without TBI develop fracture nonunions despite high bone formation in uninjured bone. Pharmacologically, the Adrb2 antagonist propranolol impairs, and the agonist formoterol promotes fracture healing in aged mice by regulating callus neovascularization. Clinically, intravenous beta-adrenergic sympathomimetics are associated with improved callus formation in trauma patients with long bone fractures. Thus, Adrb2 is a novel target for promoting bone healing, and widely used beta-blockers may cause fracture nonunion under conditions of increased sympathetic tone.

Abstract Figure

Artwork was created in BioRender.
shRNA drop-out screen identifies BRD4 targeting transcription from RNA polymerase II system to activate β-catenin to promote soft-tissue tumor proliferations
Authors: Sun Sylvia Y. , Tsiperson Vlad
Published: July 2023

BRD4 (Bromodomain containing protein 4) is a chromatin reader binds to acetylated lysine residues on histones interacting with RNA Pol II, p-TFeb. PDGF-BB was presented here, in soft-tissue tumor, as an oncogenic factor driving cell proliferation, and aberrant BRD4 knockdown significantly reduced tumor aggressiveness and unfavorable prognosis in soft-tissue tumors. To identify suppressive key drivers impeding demoid tumor growth, shRNA drop-out screen analysis identified signature of “transcription from RNA polymerase II promoter” including DDX, Stat3, SMARCA, ATM, SIRT1, cMyc that were recruited with BRD4 interation in activating β-catenin, which is a major key driver mutated in soft-tissue tumor, and its depletion ceased soft-tissue tumor cell growth. Sepcifically, BRD4 mediated PDGF-BB signaling in GSK stimulation through transcriptional regulation from RNA polymerase II activity with PI3K as target, and thus not only canonical β -catenin/TCF4 signaling, but also non-canonical β -catenin conjunction complex response was activated by BRD4 in nucleus involved in promoting cell proliferation. Our study delineated a signaling axis that may allow soft-tissue tumor cells to escape apoptosis during colonization by activating PDGFBB-BRD4-GSK-β -catenin and non-canonical-β-catenin pathway through BRD4 in cancer cells. An efficient treatment for soft-tissue tumors could be accomplished by targeting PDGF and BRD4 survival pathways on soft-tissue tumor cells.
Unveiling the role of SRY in male-biased cancers: Insights into the molecular basis of sex disparities in high-grade glioma and melanoma
Authors: Guardia Gabriela D A , Batista Rafael Loch , Penalva Luiz O. , Galante Pedro A F
Published: July 2023

Sex disparities have been observed in many tumor types affecting non-reproductive organs. Typically, the incidence and mortality rates of such cancers are higher in men. Although differences in lifestyle and environmental exposures are known contributors, knowledge of the molecular mechanisms driving sexual dimorphism in tumor development and therapy response remains limited. To address this question, we comprehensively studied the sex-determining region Y (SRY) gene, a male-specific gene that is critical in development. First, we screened 2,448 samples from 11 cancer types to identify those with a higher incidence in men and increased expression of SRY. In cases of high-grade glioma and melanoma, men with tumors exhibiting high SRY expression had a worse prognosis. Our results suggest that SRY target genes show altered expression when SRY is overexpressed. These gene sets are linked to cell growth, epithelial-mesenchymal transition, inflammation, and repression of tumor suppressor pathways. In summary, we present the first comprehensive investigation of SRY expression and its association with clinical outcomes in men with high-grade glioma and melanoma. Our results shed light on the molecular basis for sex disparities and lay the foundation for investigation of various target genes and novel cancer treatments in men with high-grade glioma and melanoma.
Reduction of ribosomal expansion segments in yeast species of theMagnusiomyces/Saprochaeteclade
Authors: Brázdovič Filip , Brejová Broňa , Siváková Barbara , Baráth Peter , Vinař Tomáš , Tomáška Ľubomír , Nosek Jozef
Published: July 2023

Ribosomes are ribonucleoprotein complexes highly conserved across all domains of life. The size differences of ribosomal RNAs (rRNAs) can be mainly attributed to variable regions termed expansion segments (ESs) protruding out from the ribosomal surface. The ESs were found to be involved in a range of processes including ribosome biogenesis and maturation, translation, and co-translational protein modification. Here, we analyze the rRNAs of the yeasts from theMagnusiomyces/Saprochaeteclade belonging to the basal lineages of the subphylum Saccharomycotina. We find that these yeasts are missing more than 400 nt from the 25S rRNA and 150 nt from the 18S rRNAs when compared to their canonical counterparts inSaccharomyces cerevisiae. The missing regions mostly map to ESs, thus representing a shift toward a minimal rRNA structure. Despite the structural changes in rRNAs, we did not identify dramatic alterations of the ribosomal protein inventories. We also show that the size-reduced rRNAs are not limited to the species of theMagnusiomyces/Saprochaeteclade, indicating that the shortening of ESs happened independently in several other lineages of the subphylum Saccharomycotina.

Significance

Expansion segments are variable regions present in the ribosomal RNAs involved in the ribosome biogenesis and translation. Although some of them were shown to be essential, their functions and the evolutionary trajectories leading to their expansion and/or reduction are not fully understood. Here, we show that the yeasts from theMagnusiomyces/Saprochaeteclade have truncated expansion segments, yet the protein inventories of their ribosomes do not radically differ from the species possessing canonical ribosomal RNAs. We also show that the loss of expansion segments occurred independently in several phylogenetic lineages of yeasts pointing out their dispensable nature. The differences identified in yeast ribosomal RNAs open a venue for further studies of these enigmatic elements of the eukaryotic ribosome.
Pinpoint: trajectory planning for multi-probe electrophysiology and injections in an interactive web-based 3D environment
Authors: Birman Daniel , Yang Kenneth J. , West Steven J. , Karsh Bill , Browning Yoni ,   the International Brain Laboratory, Siegle Joshua H. , Steinmetz Nicholas A.
Published: July 2023

Targeting deep brain structures during electrophysiology and injections requires intensive training and expertise. Even with experience, researchers often can’t be certain that a probe is placed precisely in a target location and this complexity scales with the number of simultaneous probes used in an experiment. Here, we presentPinpoint, open-source software that allows for interactive exploration of stereotaxic insertion plans. Once an insertion plan is created, Pinpoint allows users to save these online and share them with collaborators. 3D modeling tools allow users to explore their insertions alongside rig and implant hardware and ensure plans are physically possible. Probes in Pinpoint can be linked to electronic micro-manipulators allowing real-time visualization of current brain region targets alongside neural data. In addition, Pinpoint can control manipulators to automate and parallelize the insertion process. Compared to previously available software, Pinpoint’s easy access through web browsers, extensive features, and real-time experiment integration enable more efficient and reproducible recordings.
Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection
Authors: Aiyer Sriram , Baldwin Philip R. , Tan Shi Min , Shan Zelin , Oh Juntaek , Mehrani Atousa , Bowman Marianne E , Louie Gordon , Passos Dario Oliveira , Đorđević-Marquardt Selena , Mietzsch Mario , Hull Joshua A. , Hoshika Shuichi , Barad Benjamin A. , Grotjahn Danielle A. , McKenna Robert , Agbandje-McKenna Mavis , Benner Steven A. , Noel Joseph A. P. , Wang Dong , Tan Yong Zi , Lyumkis Dmitry
Published: July 2023

Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting “preferred orientations” on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle for dataset acquisition. These data reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
Transcriptomic response in pyroxsulam-resistant and susceptibleBromus sterilisidentified three distinct mechanisms of resistance
Authors: Sen Madhab Kumar , Hamouzová Katerina , Onkokesung Nawaporn , Menendez Julio , Torra Joel , Košnarová Pavlina , Sellamuthu Gothandapani , Gupta Aayushi , Bharati Rohit , Sur Vishma Pratap , Roy Amit , Soukup Josef
Published: July 2023

Bromus sterilishas evolved into a more predominant weed in the Czech Republic’s winter wheat fields, owing largely to the widespread application of pyroxsulam for its management. In this study, we report a biotype that has developed resistance to pyroxsulam and has also shown cross- resistance to other herbicides. Although no differences in ploidy levels or no mutations of acetolactate synthase (ALS) were detected, a significant elevation of ALS enzyme activity was observed in the R biotype. Through combined analysis of enzyme inhibition and total transcript expression (RNA-Seq), we have identified differentially expressed transcripts that potentially contribute to pyroxsulam metabolism. Furthermore, we observed a significant increase in the expression of genes involved in redox mechanisms and transporters that could contribute to enhanced resistance to pyroxulam in the R biotype. Our results present a novel understanding of herbicide resistance inB. sterilisthrough three distinct resistance mechanisms (ALSgene overexpression, enhanced metabolism and reduced translocation) without mutation in the herbicide target protein. This understanding is the foundation for improving management strategies for herbicide resistantB. sterilis.
Phosphorylation modulates estrogen receptor disorder by altering long-range hydrophobic interactions
Authors: Du Zhanwen , Wang Han , Wu Chen , Buck Matthias , Zheng Wenwei , Hansen Alexandar L. , Kao Hung-Ying , Yang Sichun
Published: July 2023

Protein intrinsic disorder is coupled to a range of biological phenomena, from gene regulation to cancer progression. Phosphorylation of the estrogen receptor (ER) at Ser118 through its disordered N-terminal domain (NTD) activates its transcriptional function, but it is challenging to rationalize how this modification regulates ER activity. Using biophysical approaches of small-angle X-ray scattering and nuclear magnetic resonance spectroscopy, we demonstrate that Ser118 phosphorylation triggers long-range conformational changes in ER-NTD, particularly between two hydrophobic clusters of residual structures. Alanine substitution of hydrophobic amino acids near Ser118 produces similar conformational alterations and rescues impaired ER activity caused by a phosphorylation-deficient mutant. These findings establish a direct link between phosphorylation-induced conformational changes and the activation function of this disordered protein as a promising avenue to block ER transcriptional activation.
Reinforcement learning-guided control strategies for CAR T-cell activation and expansion
Authors: Ferdous Sakib , Shihab Ibne Farabi , Chowdhury Ratul , Reuel Nigel F.
Published: July 2023

Reinforcement learning (RL), a subset of machine learning (ML), can potentially optimize and control biomanufacturing processes, such as improved production of therapeutic cells. Here, the process of CAR-T cell activation by antigen presenting beads and their subsequent expansion is formulatedin-silico. The simulation is used as an environment to train RL-agents to dynamically control the number of beads in culture with the objective of maximizing the population of robust effector cells at the end of the culture. We make periodic decisions of incremental bead addition or complete removal. The simulation is designed to operate in OpenAI Gym which enables testing of different environments, cell types, agent algorithms and state-inputs to the RL-agent. Agent training is demonstrated with three different algorithms (PPO, A2C and DQN) each sampling three different state input types (tabular, image, mixed); PPO-tabular performs best for this simulation environment. Using this approach, training of the RL-agent on different cell types is demonstrated, resulting in unique control strategies for each type. Sensitivity to input noise (sensor performance), number of control step interventions, and advantage of pre-trained agents are also evaluated. Therefore, we present a general computational framework to maximize the population of robust effector cells in CAR-T cell therapy production.

Author Summary

Custom control strategies for expansion and activation of patient-specific CAR T-cell therapies resolved by reinforcement learning using a simulation environment and updatable cell growth parameters.
Rapid identification of key genes for the rod-shaped morphology in bacteria using multi-species genomes
Authors: Liu Qi , Liu Haida , Xu Chuangchuang , Shi Jianqiang , Xie Yanghe , Hu Shunli , Han Guomin
Published: July 2023

Accurate identification of key genes is pivotal in biological research. Here, we introduce machine learning to the field of functional gene identification, enabling precise prediction of bacterial shape based on genomic information. Our machine learning model successfully predicts bacterial shape, and we determine the influence of various protein domains on shape using the model. This approach facilitates the identification of candidate genes involved in regulating bacterial shape. Through targeted knockout experiments on eight potential key regulatory genes (pal, yicC, mreB, tolQ, ftsX, amiC, yddB, andrpoZ) inEscherichia coli, we observe significant alterations in rod-shaped morphology upon individual knockout ofpalandmreBgenes.E. colitransitions from rod-shaped to spherical or cell wall-deficient protoplasmic states. Experimental validations validate the robustness of our newly developed method. This study establishes an innovative avenue for exploring functional genes, harnessing large-scale genomic information to promptly uncover key genes governing shared traits across species.
Tyk2-mediated signaling promotes the development of autoreactive CD8+CTLs and autoimmune type 1 diabetes
Authors: Mine Keiichiro , Nagafuchi Seiho , Akazawa Satoru , Abiru Norio , Mori Hitoe , Kurisaki Hironori , Yoshikai Yasunobu , Takahashi Hirokazu , Anzai Keizo
Published: July 2023

Tyrosine kinase 2 (TYK2), a member of the JAK family, might be a susceptibility gene for type 1 diabetes (T1D), whereas its precise role in autoimmune T1D remains unknown. We showedTyk2deficiency and inhibition suppressed autoimmune T1D development in non-obese diabetic (NOD) mice. Defective IL-12 signaling due toTyk2deficiency in islet-autoreactive CD8+CTLs during their priming reduced T-bet expression, leading to impaired Cxcr3 expression and effector functions against β-cells.Tyk2deficient CD8+resident dendritic cells (rDC) exhibited reduced MHC I expression and impaired cross-priming of CTLs. In β-cells, increased expressions ofFas, MHC I, and chemokines with age were attenuated byTyk2deficiency. We demonstrated that treatment with BMS-986165, a Tyk2 inhibitor, inhibited the development of CTLs and inflammation in β-cellsin vitro. BMS-986165 reduced the incidence of diabetes in NOD mice. Thus, we demonstrated that Tyk2-mediated signaling has a critical role in the development of autoreactive CD8+CTLs, inflammation in β-cells, and the pathogenesis of autoimmune T1D.

We demonstrated that Tyk2-mediated signaling plays a critical role in the development of autoreactive CD8+CTLs, inflammation in β-cells, and the pathogenesis of autoimmune T1D. These findings will lead to the development of safety and effective prevention strategies for T1D.
KDM4-dependent DNA breaks at active promoters facilitate +1 nucleosome eviction
Authors: Imre László , Nánási Péter , Szatmári István , Kókai Endre , Austin Caroline A. , Dombrádi Viktor , Szabó Gábor
Published: July 2023

When the effect of various posttranslational histone tail modifications (PTMs) on nucleosome stability was compared in anin situassay involving agarose-embedded nuclei, the promoter proximal H3K4me3, H3K27ac and H4K8ac positive nucleosomes exhibited relative sensitivity to intercalators as compared to bulk H3-GFP or nucleosomes carrying any of the following marks: H3K27me1, H3K27me2, H3K27me3, H3K9me1, H3K9me2, H3K9me3, H3K36me3, H3K4me0, H3K4me1, H3K4me2, H3K9ac, and H3K14ac. Nickase or DNase I treatment of the nuclei, or bleomycin treatment of live cells, did not affect the stability of nucleosomes carrying H3K4me3 or H3K27ac, while those of the second group were all destabilized upon treatment with intercalators. These observations support the possibility that the promoter proximal marks specify dynamic nucleosomes accomodating relaxed DNA sequences due to DNA breaks generatedin vivo. In line with this interpretation, endogeneous, 3’OH nicks were mapped within the nucleosome free region of promoters controlling genes active in human mononuclear cells, a conclusion supported by superresolution colocalization studies. The +1 nucleosomes were stabilized and the incidence of nicks was decreased at the promoters upon KDM4a,b,c KO induction (Pedersen et al, EMBO J, 2016) in mouse embryonic stem cells (mES). While etoposide did not further destabilize +1 nucleosomes in control mES, their stabilized state in the KO state was reversed by the drug. A significant fraction of the DNA breaks comprises TOP2-generated nicks according to the results of molecular combing experiments. The chromatin regions harboring nicks are topologicaly separated from the domains containing superhelical chromatin. These observations lend support for a model where the role of DNA strand discontinuities in transcriptional regulation and in higher-order chromatin organization are integrated.
Linear modeling of brain activity during selective attention to continuous speech: the critical role of the N1 effect in event-related potentials to acoustic edges
Authors: Mai Adrian , Hillyard Steven A. , Strauss Daniel J.
Published: July 2023

Recent work in the field of neural speech tracking provided evidence for a cortical rep-resentation of speech through superposition of event-related responses to acoustic edges, an idea closely related to the popular linear modeling approach to study cortical syn-chronization to speech via magneto- or electroencephalography (M/EEG). However, it is still unclear to what extent speech-evoked event-related potentials (ERPs) including well-established phenomena, e.g., the N1 selective attention effect, contribute to the regression-based analyses. Here, we addressed this question by analyzing an EEG dataset obtained during a simple multispeaker selective attention task in which participants were cued to attend to only one of two competing speakers. Segmenting the ongoing EEG based on acoustic edges, we were able to replicate previous findings of event-related responses to speech in MEG data with particularly clear P1-N1-P2 complexes. Crucially, speech-evoked ERPs exhibited significant effects of attention in line with the auditory N1 effect. Comparing speech-evoked ERPs to the linear regression results revealed two major find-ings. First, temporal response functions (TRFs) obtained from forward modeling were strongly temporally as well as spatially correlated with corresponding true ERPs. Sec-ond, effects of attention demonstrated by the stimulus reconstruction (SR) accuracies obtained from backward modeling appeared to be driven by a consistent generation of speech-evoked ERPs including the N1 effect. Taken together, our observations reveal a direct link between ERPs to acoustic edges in speech and the linear TRF and SR mod-eling techniques. We emphasize the enhancement in signal-to-noise ratio provided by repeatedly evoked N1 responses to be a critical factor in facilitating the tracking and subsequent higher-order processing of selectively attended speech. In addition to that, the findings imply a cortical speech representation through superimposed speech-evoked ERPs in accordance with recent arguments promoting the neural evoked-response speech tracking model.
A high-quality reference genome for the common creek chub,Semotilus atromaculatus
Authors: Meuser Amanda V. , Pitura Amy R. , Mandeville Elizabeth G.
Published: July 2023

Creek chub (Semotilus atromaculatus) are a leuciscid minnow species commonly found in anthropogenically disturbed environments, making them an excellent model organism to study human impacts on aquatic systems. Genomic resources for creek chub and other leuciscid species are currently limited. However, advancements in DNA sequencing now allow us to create genomic resources at a historically low cost. Here, we present a high quality 239 contig reference genome for the common creek chub, created with PacBio HiFi sequencing. We compared the assembly quality of two pipelines: Pacific Biosciences’ Improved Phase Assembly (IPA; 873 contigs) and Hifiasm (239 contigs). Quality and completeness of this genome is comparable to the zebrafish (Danioninae) and fathead minnow (Leuciscidae) genomes. The creek chub genome is highly syntenic to the zebrafish and fathead minnow genomes, and while our assembly does not resolve into the expected 25 chromosomes, synteny with zebrafish suggests that each creek chub chromosome is likely represented by 1-4 large contigs in our assembly. This reference genome is a valuable resource that will enhance genomic bio-diversity studies of creek chub and other non-model leuciscid species common to disturbed environments.
Genetic dissection of BDNF and TrkB expression in glial cells
Authors: Niu Changran , Yue Xinpei , An Juan Ji , Xu Haifei , Xu Baoji
Published: July 2023

The brain-derived neurotrophic factor (BDNF) and its high-affinity receptor tropomyosin-related kinase receptor B (TrkB) are widely expressed in the central nervous system. It is well documented that neurons express BDNF and full-length TrkB (TrkB.FL), and a lower level of truncated TrkB (TrkB.T). With conflicting results, glial cells also have been reported to express BDNF and TrkB. In the current study, we employed a more sensitive and reliable genetic method to characterize the expression of BDNF and TrkB in glial cells in the mouse brain. We utilized three Cre mouse strains in which Cre recombinase is expressed in the same cells as BDNF, TrkB.FL, or all TrkB isoforms, and crossed them to Cre-dependent EGFP reporter mice to label BDNF- or TrkB-expressing cells. We performed immunohistochemistry with glial cell markers to examine the expression of BDNF and TrkB in microglia, astrocytes, and oligodendrocytes. Surprisingly, we found no BDNF- or TrkB-expressing microglia in the brain and spinal cord. Consistent with previous studies, most astrocytes only express TrkB.T in the adult brain. Moreover, there are a small number of astrocytes and oligodendrocytes that express BDNF, the function of which is to be determined. We also found that oligodendrocyte precursor cells, but not mature oligodendrocytes, express both TrkB.FL and TrkB.T in the adult brain. These results not only clarify the expression of BDNF and TrkB in glial cells, but also open opportunities to investigate previously unidentified roles of BDNF and TrkB in glial cells.