bluuebunny/crossref_metadata_2025_split huggingface dataset:
Poorer longitudinal growth among HIV exposed compared to unexposed infants in Kenya
Authors: Glass Delaney J. , Kinge Maureen , Njuguna Irene , McGrath Christine J. , Lawley Kendall , Moraa Hellen , Onyango Alvin , Wamalwa Dalton , Shattuck Eric , Enquobahrie Daniel A. , John-Stewart Grace 
Published: December 2024

Background:
Most infants born to women living with HIV (WLH) are HIV-exposed but uninfected exposed infants have poorer growth than HIV-unexposed uninfected children. Few large studies have compared children who are exposed (CHEU) and unexposed (CHUU) in the era of dolutegravir (DTG)-based antiretroviral treatment (ART).

Setting:
Longitudinal study of mother-infant CHEU and CHUU pairs in Nairobi and Western Kenya.

Methods:
Mother-infant pairs were enrolled at 6 weeks postpartum with 6-monthly growth assessments. We compared longitudinal growth between CHEU and CHUU infants during the first year and assessed biological and social factors affecting growth (length and weight-for-age z-scores [LAZ, WAZ] and weight for length z-scores [WLZ]) and stunting (LAZ<-2), underweight (WAZ<-2), and wasting (WLZ<-2) from birth to 1 year.

Results:
Among 2000 infants (1000 CHEU and 1000 CHUU), CHEU infants had significantly lower LAZ at 6 months (-0.165 (95% CI: -0.274, -0.056), p-value = 0.003) and 12 months (-0.195, 95% CI:-0.294, -0.095, p-value = 0.0001; n = 1616). CHEU infants had a higher prevalence of stunting at 6 months compared to CHUU infants (Prevalence Ratio: 1.45, 95% CI: 1.14, 1.85). Among all children, greater maternal BMI, education, and caregiver-perceived social support were positively associated with growth. Higher maternal and infant comorbidities were associated with growth deficits for CHEU infants. Among CHEU, ART timing (before versus during pregnancy) and ART regimen (dolutegravir(DTG)-based, efavirenz-based, and protease inhibitor/other) did not affect growth.

Conclusion:
Growth deficits among CHEU persist, despite DTG-based ART. Addressing comorbidities, amplifying social support, and education may improve growth outcomes.
Ultra High-Frequency Ultrasound of Median Nerve Fascicles at the Wrist in Amyotrophic Lateral Sclerosis: An Exploratory Study
Authors: Meiling James B. , Caress James B. , Cartwright Michael S. 
Published: December 2024

Purpose:
High-frequency ultrasound (HFUS) of muscle and nerve has the potential to be a reliable, responsive, and informative biomarker of disease progression for individuals with amyotrophic lateral sclerosis (ALS). High-frequency ultrasound is not able to visualize median nerve fascicles to the same extent as ultra-high-frequency ultrasound (UHFUS). Evaluating the number and size of fascicles within a nerve may facilitate a better understanding of nerve diseases. This exploratory study aims to image median nerve fascicles at the wrist in individuals with ALS using UHFUS and compare these findings with those from previously observed controls.

Methods:
Fifteen individuals with ALS underwent sonographic examination of the median nerves on each upper limb using UHFUS with a 48-MHz linear array transducer. Fascicle count and density in each examined nerve were determined by a single rater. Demographic and sonographic data from 20 previously studied controls were compared.

Results:
In individuals with ALS, the average fascicle number was 22.4 (SD 5.2) and average fascicle density 1.7 (SD 0.5). There was no significant difference in fascicle counts between individuals with ALS and controls.

Conclusions:
Fascicular quantification using UHFUS is possible in individuals with ALS. Given the lack of appreciable difference between fascicle counts in individuals with ALS and controls, UHFUS of the median nerve at the wrist may not be a responsive biomarker for ALS disease progression.
Structure-guided engineering of α-ketoisocaproate dioxygenase increases isobutene production inSynechocystissp. PCC 6803
Authors: Schumann Conrad , Kugler Amit , Shah Bhavik , Berggren Gustav , Land Henrik , Blikstad Cecilia , Stensjö Karin 
Published: December 2024

AbstractIsobutene is a promising precursor for jet fuel due to its high energy density and favorable combustion properties. Light-driven bioproduction of isobutene has recently been investigated as an alternative strategy to crude oil refinement or fermentation-based manufacturing processes by harnessing the unicellular cyanobacteriumSynechocystissp. PCC 6803 and the α-ketoisocaproate dioxygenase (RnKICD) fromRattus norvegicus. However, the obtained production level was not sufficient, partially due the promiscuous activity ofRnKICD. The enzyme catalyzes both the reaction with ρ-hydroxyphenylpyruvate (HPP) for homogentisate formation, as well as the reaction with α-ketoisocaproate (KIC), the precursor for isobutene synthesis. Here, to overcome this bottleneck step in the isobutene biosynthesis, protein engineering was employed to improveRnKICD activity and in vivo isobutene production. PurifiedRnKICD variants were characterized by measuring in vitro KIC and HPP consumption rates, as well as isobutene formation rate. The active site mutations F336V, N363A altered the KIC and HPP consumption rates, while the KIC-to-isobutene conversion ratio was only marginally affected. Besides, theRnKICD variants F336V, N363A and F336V/N363A exhibited a substantially enhanced substrate selectivity for KIC over HPP. Among the examined engineeredSynechocystisstrains, Syn-F336V showed a 4-fold improvement in isobutene production, compared to the base strain (Syn-RnKICD). Our findings reveal that residues F336 and N363 play a crucial role in substrate interactions, as targeted mutations at these sites shifted the substrate selectivity towards KIC and elevated the in vivo isobutene production levels significantly. We conclude that engineering the active site ofRnKICD is a potent tool for improving isobutene bioproduction inSynechocystis.HighlightsPromiscuous α-ketoisocaproate dioxygenase (KICD) fromRattus norvegicuswas overproduced inSynechocystissp. PCC 6803.Protein engineering was used to improve substrate selectivity.The generated F336V variant led to a 4-fold increase in isobutene productionin vivo.
Hemin-binding DNA structures on the surface of bacteria promote extracellular electron transfer
Authors: Ajunwa Obinna M. , Minero Gabriel Antonio S. , Jensen Sissel D. , Meyer Rikke L. 
Published: December 2024

ABSTRACTRecent research has shown that bacteria in anoxic layers ofPseudomonas aeruginosabiofilms can respire by transferring electrons to oxygen via extracellular DNA (eDNA) and DNA- binding redox mediators that are unique to this species1. In this study, we propose a similar but generic mechanism by which bacteria can transfer electrons via DNA in biofilms, using hemin as a redox-mediator and hemin-binding G-quadruplex (G4) DNA structures in the extracellular matrix.UsingStaphylococcus epidermidisas a model organism, voltammetry showed that eDNA and hemin were needed for extracellular electron transfer (EET). Surface-associated G4-DNA formed a complex with hemin, which transferred electrons from the bacteria to an electrode under anoxic conditions. Addition of G4-DNA and hemin to growing biofilms promoted EET which was stable for days. G4-DNA/hemin is also a peroxidase-like DNAzyme, capable of transferring electrons from bacteria to H2O2.G4-DNA were only recently discovered to be abundant in the extracellular matrix of biofilms2,3. We now show that hemin turns these structures into conduits for EET. The study opens the door to new and generic mechanisms for bacterial energy conservation under oxygen- limiting conditions, and for tackling H2O2, a common host defense mechanism against bacterial infections.
Chronic Obstructive Pulmonary Disease Prediction Using Deep Convolutional Network
Authors: Alve Shahran Rahman , Mahmud Muhammad Zawad , Islam Samiha , Khan Mohammad Monirujjaman 
Published: December 2024

AbstractAI and deep learning are two recent innovations that have made a big difference in helping to solve problems in the clinical space. Using clinical imaging and sound examination, they also work on improving their vision so that they can spot diseases early and correctly. Because there aren’t enough trained HR, clinical professionals are asking for help with innovation because it helps them adapt to more patients. Aside from serious health problems like cancer and diabetes, the effects of respiratory infections are also slowly getting worse and becoming dangerous for society. Respiratory diseases need to be found early and treated quickly, so listening to the sounds of the lungs is proving to be a very helpful tool along with chest X-rays. The presented research hopes to use deep learning ideas based on Convolutional Brain Organization to help clinical specialists by giving a detailed and thorough analysis of clinical respiratory sound data for Ongoing Obstructive Pneumonic identification. We used MFCC, Mel-Spectrogram, Chroma, Chroma (Steady Q), and Chroma CENS from the Librosa AI library in the tests we ran. The new system could also figure out how serious the infection was, whether it was mild, moderate, or severe. The test results agree with the outcome of the deep learning approach that was proposed. The accuracy of the framework arrangement has been raised to a score of 96% on the ICBHI. Also, in the led tests, we used K-Crisp Cross-Approval with ten parts to make the presentation of the new deep learning approach easier to understand. With a 96 percent accuracy rate, the suggested network is better than the rest. If you don’t use cross-validation, the model is 90% accurate.
Do-it-yourselfde novoantibody sequencing workflow that achieves complete accuracy of the variable regions
Authors: He Meng-Ting , Li Ning , Wang Jian-Hua , Wei Zhi-Zhong , Feng Jie , Li Wen-Ting , Sui Jian-Hua , Huang Niu , Dong Meng-Qiu 
Published: December 2024

ABSTRACTAntibodies are widely used as research tools or therapeutic agents. Knowing the sequences of the variable regions of an antibody—both the heavy chain and the light chain—is a prerequisite for the production of recombinant antibodies. Mass spectrometry-basedde novosequencing is a frequently used, and sometimes the only approach to gaining this information. Here, we describe a workflow that enables accurate sequence determination of monoclonal antibodies based on mass spectrometry data and freely available software tools. This workflow, which we developed using a homemade anti-FLAG monoclonal antibody as a reference sample, achieved 100% accuracy of the variable regions with clear distinction between leucine (L) and isoleucine (I). Using this workflow, we successfully decoded a monoclonal anti-HA antibody, for which we had no prior knowledge of its sequence. Based on thede novosequencing result, we generated a recombinant anti-HA antibody, and demonstrated that it has the same specificity, sensitivity, and affinity as the commercial antibody.Abstract Figure
LPS-induced sepsis disrupts brain activity in a region- and vigilance-state specific manner
Authors: Leemburg Susan , Kala Annu , Nataraj Athira , Karkusova Patricia , Baindur Siddharth , Suresh Amritesh , Blahna Karel , Jezek Karel 
Published: December 2024

AbstractSepsis-associated encephalopathy (SAE) is a common complication of sepsis and the systemic inflammatory response syndrome that leads to lasting consequences in survivors. It manifests as early EEG changes, that are region-, time- and state-specific, possibly reflecting distinct mechanisms of injury.Here, we investigated the effects of 5mg/kg lipopolysaccharide (LPS) on hippocampal and cortical sleep-wake states, oscillatory and non-oscillatory neuronal activity, as well as on within and between state dynamics using state-space analysis.LPS induced rapid-onset severe temporal and spatial vigilance state fragmentation, which preceded all other spectral changes by ∼90 minutes. Thereafter, LPS led to specific destabilization and increased delta oscillatory activity in wakefulness, but not NREM sleep, although state transitions remained largely normal. Instead, reduced NREM delta power resulted from aperiodic spectrum changes. LPS specifically reduced higher frequency hippocampal gamma oscillations (60-80Hz peak) in wakefulness, but not cortical high gamma or lower frequency gamma oscillations.These results suggest that disruption of sleep-wake patterns could serve as an early indicator of sepsis and associated encephalopathy, independent of spectral changes. Moreover, treatment aimed at stabilizing vigilance states in early stages of sepsis might prove to be a novel option preventing the development of further pathological neurophysiology, as well as limiting inflammation-related brain damage.
Stress-induced organismal death is genetically regulated by the mTOR-Zeste-Phae1 axis
Authors: Matsumura Takashi , Ryuda Masasuke , Matsumoto Hitoshi , Kamiyama Takumi , Kondo Shu , Nakamura Akira , Hayakawa Yoichi , Niwa Ryusuke 
Published: December 2024

AbstractAll organisms are exposed to various stressors, which can sometimes lead to organismal death, depending on their intensity. While stress-induced organismal death has been observed in many species, the underlying mechanisms remain unclear. In this study, we investigated the molecular mechanisms of stress-induced organismal death in the fruit flyDrosophila melanogaster. We identified a chymotrypsin-like serine proteasePhaedra1(Phae1) as a death mediator inD. melanogasterlarvae.Phae1expression was upregulated by lethal heat stress (40 °C) but not non-lethal heat stress (38 °C or lower). The most prominent induction ofPhae1occurred in the central nervous system (CNS). We found neuro-specific knockdown ofPhae1increased survival and reduced neuronal caspase activity following exposure to lethal heat stress, suggesting that the transcriptional upregulation ofPhae1in the CNS is essential for stress-induced organismal death. We next found via bioinformatic and biochemical analyses that the transcription factor Zeste (Z) bound thePhae1enhancer region and thatzloss-of-function impairedPhae1induction in the CNS, increasing survival following lethal heat stress. In addition, we found via chemical screening that rapamycin, a chemical inhibitor of mechanistic target of rapamycin (mTOR), suppressedPhae1expression. Neuro-specific knockdown ofmTorreduced the protein levels of both Phae1 and Z, leading to an increase in survival following lethal heat stress. Together, these results indicate that heat stress-induced organismal death inD. melanogasterlarvae is regulated by a genetically encoded transcriptional signaling pathway involving the mTOR-Z-Phae1 axis.
A novel newborn screening modality: Non-targeted proteome analysis using low-cost iron powders
Authors: Nakajima Daisuke , Ishikawa Masaki , Konno Ryo , Sasai Hideo , Ohara Osamu , Kawashima Yusuke 
Published: December 2024

AbstractIn this study, we developed a simple protein extraction method for dried blood spots (DBS) that potentially meets the throughput required for newborn screening (NBS) and optimizes non-targeted proteomic analysis in combination with liquid chromatography coupled mass spectrometry in the data-independent-acquisition mode (DIA-LC-MS/MS). The developed pipeline, termedNon-targetedAnalysis ofNon-specificallyDBS-Absorbed proteins (NANDA), successfully addressed the following three challenges: (1) processing of 96 3.2-mm DBS punches in parallel using low-cost iron powders with a robotic system, (2) identifying more than 5,000 proteins using DIA-LC-MS/MS, and (3) improving DIA-LC-MS/MS throughput to 40 samples/day with minimal compromise in protein coverage depth. The results imply that this pipeline can open new venues for conducting NBS using non-targeted quantitative proteome profiling, which has been a currently missing modality in NBS.
Target deconvolution of an insulin hypersecretion-inducer acting through VDAC1 with a distinct transcriptomic signature in beta-cells
Authors: Roy Gitanjali , Ordóñez Andrea , Binns Derk D. , Rodrigues dos Santos Karina , Kwakye Michael B. , King George C. , Mukherjee Noyonika , Templin Andrew T. , Tan Zhiyong , Richardson Timothy I. , Doud Emma H. , Mosley Amber L. , Emfinger Christopher H. , Attie Alan D. , Keller Mark P. , Johnson Travis S. , Kalwat Michael A. 
Published: December 2024

ABSTRACTObesity, insulin resistance, and a host of environmental and genetic factors can drive hyperglycemia, causing β-cells to compensate by increasing insulin production and secretion. In type 2 diabetes (T2D), β-cells under these conditions eventually fail. Rare β-cell diseases like congenital hyperinsulinism (HI) also cause inappropriate insulin secretion, and some HI patients develop diabetes. However, the mechanisms of insulin hypersecretion and how it causes β-cell dysfunction are not fully understood. We previously discovered small molecules (e.g. SW016789) that cause insulin hypersecretion and lead to a loss in β-cell function without cell death. Here, we uncover the protein target of SW016789 and provide the first time-course transcriptomic analysis of hypersecretory responses versus thapsigargin-mediated ER stress in β-cells. In mouse MIN6 and human EndoC-βH1 β-cells, we identified and validated VDAC1 as a SW016789 target using photoaffinity proteomics, cellular thermal shift assays, siRNA, and small molecule inhibitors.SW016789 raises membrane potential to enhance Ca2+influx, potentially through VDAC1. Chronically elevated intracellular Ca2+appears to underpin the negative impacts of hypersecretion, as nifedipine protected against each small molecule hypersecretion inducer we tested. Using time- course RNAseq, we discovered that hypersecretion induced a distinct transcriptional pattern compared to ER stress. Clustering analyses led us to focus on ER-associated degradation (ERAD) as a potential mediator of the adaptive response. SW016789 reduced the abundance of ERAD substrate OS-9 and pharmacological inhibition of ERAD worsened β-cell survival in response to hypersecretory stress. Changes in other ERAD components in MIN6 and EndoC-βH1 at the protein level were minor with either SW016789 or thapsigargin. However, immunostaining for core ERAD components SEL1L, HRD1, and DERL3 in non-diabetic and T2D human pancreas revealed altered distributions of SEL1L/HRD1 and SEL1L/DERL3 rations in β-cells of T2D islets, in alignment with altered ERAD in stressed β-cells. We conclude that hypersecretory stimuli, including SW016789- mediated VDAC1 activation, cause enhanced Ca2+influx and insulin release. Subsequent differential gene expression represents a β-cell hypersecretory response signature that is reflected at the protein level for some, but not all genes. A better understanding of how β-cells induce hypersecretion and the mechanisms of negative feedback on secretory rate may lead to the discovery of novel therapeutic targets for T2D and HI.
Retinal organoids mirror CRISPR/Cas9 gene editing efficiency observed in vivo
Authors: Pulman Juliette , Malki Hugo , Oudin Paul , Aydin Ecem , Tran Sophie , Visticot Laura , Robert Camille , De Cian Anne , As Marie , Goureau Olivier , Concordet Jean-Paul , Dalkara Deniz 
Published: December 2024

AbstractHuman retinal organoids arein vitro3D structures that recapitulate key molecular and structural characteristics of thein vivoretina. They include the presence of all essential retinal cell types including photoreceptors, making them relevant models for preclinical development of gene therapies. A critical knowledge gap exists in understanding their utility for gene editing optimization, particularly for specific genetic disorders. We assessed the potential of retinal organoids for optimizing CRISPR/Cas9-mediated gene editing, focusing on the therapeutically relevantRHOgene implicated in autosomal dominant Retinitis Pigmentosa (adRP). Using retinal organoids,in vitroHEK293T cells, and two humanized mouse models carrying differentRHOmutations, we compared editing efficiencies. We observed that retinal organoids have lower transfection efficiency compared to HEK293T cells. Notably, they exhibited editing efficiencies more closely aligned with those foundin vivo. We also observed similar delivery patterns of CRISPR/Cas9 tools in both retinal organoids and mouse retinas. These delivery patterns and editing efficiencies remained consistent across dual AAV systems and transiently delivered ribonucleoprotein complexes. Our findings demonstrate that retinal organoids achieve editing outcomes comparable to those observedin vivounderscoring their utility as part of a preclinical testing platform for genome editing, with implications for advancing gene therapy research in inherited retinal diseases.Graphical abstracteTOCRetinal organoids can be used to mirrorin vivomouse retina to develop CRISPR therapeutics. Here, Pulman and colleagues show similar ranges of gene editing and delivery dynamics between the organoids andin vivomouse retina, highlighting the organoid’s underexplored potential for evaluating gene editing therapies in retinal diseases.
Ultrastructural membrane dynamics of mouse and human cortical synapses
Authors: Eddings Chelsy R. , Fan Minghua , Imoto Yuuta , Itoh Kie , McDonald Xiomara , Eilers Jens , Anderson William S. , Worley Paul F. , Lippmann Kristina , Nauen David W. , Watanabe Shigeki 
Published: December 2024

SummaryLive human brain tissues provide unique opportunities for understanding the physiology and pathophysiology of synaptic transmission. Investigations have been limited to anatomy, electrophysiology, and protein localization—while crucial parameters such as synaptic vesicle dynamics were not visualized. Here we utilize zap-and-freeze time-resolved electron microscopy to overcome this hurdle. First we validate the approach with acute mouse brain slices to demonstrate that axons parallel to the electrical field can be stimulated to produce calcium signaling. Next we show that ultrafast endocytosis is induced and can be captured in both mouse and human brain slices. Crucially, in both species a protein essential for ultrafast endocytosis Dynamin 1xA (Dyn1xA) localizes to the region peripheral to the active zone, the putative endocytic zone, indicating a likely mechanism conservation between mouse and human. This approach has the potential to reveal dynamic, high-resolution information about synaptic membrane trafficking in intact human brain slices.