bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacteriophages as an alternative for biofilm eradication in Klebsiella Pneumonia Strains.
Authors: Chipurupalli Alikya , Rathore Rohit , Karumidze Natia 
Published: July 2023

Background -Biofilms are a cause for a variety of infectious diseases given its abundant existence throughout nature. With the help of biofilm, the pathogenic bacteria are protected from unfavorable environments and conditions like extreme pH and temperature, high salinity, UV radiation. Most importantly is that it increases the resistance to antibiotics by 1000 times. Antimicrobial resistance has serious consequences not only in health care but also in food processing, drinking water distribution system, the paper industry, and others.

Materials and Methods – In our study were used three K. pneumoniae (kp41, kp42, kp47), and two P. aeruginosa strains (PA315, PA88). Klebsiella pneumoniae and P. aeruginosa specific bacteriophages (vB-kB-41, vB-Kp-42, vB-kp-47, vB-Psa-315, and vB-Psa-88) were used to test the formation of biofilm by using the Microtiter plate method (TCP) and Tube method (TM).

Results – All the tested bacteria showed to form biofilms in tubes, while on 96 well plates we could observe obvious biofilm with P.aeruginosa N88. With both methods, we had biofilm reduction that was treated with appropriate bacteriophages and incubated for 24 hours.

Conclusion- Emerging antimicrobial resistance needs to be addressed before we run out of our potential antibiotics. Usage of biofilms can be one of the alternatives to effectively and specifically treat these serious gram-negative infections. A more standardized approach should be established for identification of such specific bacteriophage strains which curb the bacterial growth efficiently.
The proteolysis of ZP proteins is essential to control cell membrane structure and integrity of developing tubes
Authors: Drees Leonard , Riedel Dietmar , Schuh Reinhard , Behr Matthias 
Published: July 2023

AbstractMembrane expansion integrates multiple forces to mediate precise tube growth and network formation. Defects lead to deformations, as found in diseases such as polycystic kidney diseases, aortic aneurysms, stenosis, and tortuosity. We identified a mechanism of sensing and responding to the membrane expansion of tracheal tubes. We show inDrosophilathat Zona Pellucida domain proteins Piopio and Dumpy cooperate to integrate mechanical stress at cell membranes and luminal matrix. When tension appears at the apical membrane due to tracheal tube length expansion, Piopio undergoes ectodomain shedding by the Matriptase homolog Notopleural, which releases Piopio-mediated linkages between membranes and extracellular matrix. Failure of this process leads to deformations of the apical membrane and comprises tubular network function. We also show conserved ectodomain shedding by the human matriptase during TGF-β signaling, both of which are required in the lung, providing novel approaches for in-depth analysis of pulmonary diseases caused by cell and tube shape changes.
Exploring the parity paradox: Differential effects on neuroplasticity and neuroinflammation by APOEe4 genotype at middle-age
Authors: Lee Bonnie H , Cevizci Mel , Lieblich Stephanie E , Ibrahim Muna , Wen Yanhua , Eid Rand S , Lamers Yvonne , Duarte-Guterman Paula , Galea Liisa A.M. 
Published: July 2023

AbstractFemale sex and Apolipoprotein E (APOE) ε4 genotype are top non-modifiable risk factors for Alzheimer’s disease (AD). Although female-unique experiences like parity (pregnancy and motherhood) have positive effects on neuroplasticity at middle age, previous pregnancy may also contribute to AD risk. To explore these seemingly paradoxical long-term effects of parity, we investigated the impact of parity with APOEε4 genotype by examining behavioural and neural biomarkers of brain health in middle-aged female rats. Our findings show that primiparous (parous one time) hAPOEε4 rats display increased use of a non-spatial cognitive strategy and exhibit decreased number and recruitment of new-born neurons in the ventral dentate gyrus of the hippocampus in response to spatial working memory retrieval. Furthermore, primiparity and hAPOEε4 genotype synergistically modulate neuroinflammatory markers in the ventral hippocampus. Collectively, these findings demonstrate that previous parity in hAPOEε4 rats confers an added risk to present with reduced activity and engagement of the hippocampus as well as elevated pro-inflammatory signaling, and underscores the importance of considering female-specific factors and genotype in health research.HighlightshAPOEε4 rats made more errors and used a non-spatial cognitive strategyPrimiparous hAPOEε4 rats increased use of a non-spatial cognitive strategyParity increased neurogenesis in wildtype rats, but decreased it in hAPOEε4 ratsPrimiparous hAPOEε4 rats had less active new neurons in response to memory retrievalParity and hAPOEε4 affect the neuroimmune milieu in a region-specific manner
Recombination map tailored to Native Hawaiians improves robustness of genomic scans for positive selection
Authors: Dinh Bryan L. , Tang Echo , Taparra Kekoa , Nakatsuka Nathan , Chen Fei , Chiang Charleston W. K. 
Published: July 2023

AbstractRecombination events establish the patterns of haplotypic structure in a population and estimates of recombination rates are used in several downstream population and statistical genetic analyses. Using suboptimal maps from distantly related populations may reduce the efficacy of genomic analyses, particularly for underrepresented populations such as the Native Hawaiians. To overcome this challenge, we constructed recombination maps using genome-wide array data from two study samples of Native Hawaiians: one reflecting the current admixed state of Native Hawaiians (NH map), and one based on individuals of enriched Polynesian ancestries (PNS map) with the potential to be used for less admixed Polynesian populations such as the Samoans. We found the recombination landscape to be less correlated with those from other continental populations (e.g. Spearman’s rho = 0.79 between PNS and CEU (Utah residents with Northern and Western European ancestry) compared to 0.92 between YRI (Yoruba in Ibadan, Nigeria) and CEU at 50 kb resolution), likely driven by the unique demographic history of the Native Hawaiians. PNS also shared the fewest recombination hotspots with other populations (e.g. 8% of hotspots shared between PNS and CEU compared to 27% of hotspots shared between YRI and CEU). We found that downstream analyses in the Native Hawaiian population, such as local ancestry inference, imputation, and IBD segment and relatedness detections, would achieve similar efficacy when using the NH map compared to an omnibus map. However, for genome scans of adaptive loci using integrated haplotype scores, we found several loci with apparent genome-wide significant signals (|Z-score| > 4) in Native Hawaiians that would not have been significant when analyzed using NH-specific maps. Population-specific recombination maps may therefore improve the robustness of haplotype-based statistics and help us better characterize the evolutionary history that may underlie Native Hawaiian-specific health conditions that persist today.
ScreenDMT reveals linoleic acid diols replicably associate with BMI and stimulate adipocyte calcium fluxes
Authors: Dreyfuss Jonathan M. , Djordjilovic Vera , Pan Hui , Bussberg Valerie , MacDonald Allison M. , Narain Niven R. , Kiebish Michael A. , Blüher Matthias , Tseng Yu-Hua , Lynes Matthew D. 
Published: July 2023

AbstractActivating brown adipose tissue (BAT) improves systemic metabolism, making it a promising target for metabolic syndrome. BAT is activated by 12,13-dihydroxy-9Z-octadecenoic acid (12,13-diHOME), which we previously identified to be inversely associated with BMI and which directly improves metabolism in multiple tissues. Here we profile plasma lipidomics from a cohort of 83 people and test which lipids’ association with BMI replicates in a concordant direction using our novel tool ScreenDMT, whose power and validity we demonstrate via mathematical proofs and simulations. We find that the linoleic acid diols 12,13-diHOME and 9,10-diHOME both replicably inversely associate with BMI and mechanistically activate calcium fluxes in mouse brown and white adipocytes in vitro, which implicates this pathway and 9,10-diHOME as candidate therapeutic targets. ScreenDMT can be applied to test directional mediation, directional replication, and qualitative interactions, such as identifying biomarkers whose association is shared (replication) or opposite (qualitative interaction) across diverse populations.
A microfluidic strategy to capture antigen-specific high affinity B cells
Authors: Alhassan Ahmed M. , Shirure Venktesh S. , Luo Jean , Nguyen Bryan B. , Rollins Zachary A. , Shergill Bhupinder S. , Zhu Xiangdong , Baumgarth Nicole , George Steven C. 
Published: July 2023

ABSTRACTAssessing B cell affinity to pathogen-specific antigens prior to or following exposure could facilitate the assessment of immune status. Current standard tools to assess antigen-specific B cell responses focus on equilibrium binding of the secreted antibody in serum. These methods are costly, time-consuming, and assess antibody affinity under zero-force. Recent findings indicate that force may influence BCR-antigen binding interactions and thus immune status. Here, we designed a simple laminar flow microfluidic chamber in which the antigen (hemagglutinin of influenza A) is bound to the chamber surface to assess antigen-specific BCR binding affinity of five hemagglutinin-specific hybridomas under 65- to 650-pN force range. Our results demonstrate that both increasing shear force and bound lifetime can be used to enrich antigen-specific high affinity B cells. The affinity of the membrane-bound BCR in the flow chamber correlates well with the affinity of the matched antibodies measured in solution. These findings demonstrate that a microfluidic strategy can rapidly assess BCR-antigen binding properties and identify antigen-specific high affinity B cells. This strategy has the potential to both assess functional immune status from peripheral B cells and be a cost-effective way of identifying individual B cells as antibody sources for a range of clinical applications.
Extrasynaptic localization is essential for α5GABAAreceptor modulation of dopamine system function
Authors: McCoy Alexandra M. , Prevot Thomas D. , Mian Md Yeunus , Sharmin Dishary , Ahmad Adeeba N. , Cook James M. , Sibille Etienne L. , Lodge Daniel J. 
Published: July 2023

AbstractDopamine system dysfunction, observed in animal models with psychosis-like symptomatology, can be restored by targeting Gamma-Aminobutyric Acid type A receptors (GABAAR) containing the α5, but not α1, subunit in the ventral hippocampus (vHipp). The reason for this discrepancy in efficacy remains elusive; however, one key difference is that α1GABAARs are primarily located in the synapse, whereas α5GABAARs are mostly extrasynaptic. To test whether receptor location is responsible for this difference in efficacy, we injected a small interfering ribonucleic acid (siRNA) into the vHipp to knock down radixin, a scaffolding protein that holds α5GABAARs in the extrasynaptic space. We then administered GL-II-73, a positive allosteric modulator of α5GABAARs (α5-PAM) known to reverse shock-induced deficits in dopamine system function, to determine if shifting α5GABAARs from the extrasynaptic space to the synapse would prevent the effects of α5-PAM on dopamine system function. As expected, knockdown of radixin significantly decreased radixin-associated α5GABAARs and increased the proportion of synaptic α5GABAARs, without changing the overall expression of α5GABAARs. Importantly, GL-II-73 was no longer able to modulate dopamine neuron activity in radixin-knockdown rats, indicating that the extrasynaptic localization of α5GABAARs is critical for hippocampal modulation of the dopamine system. These results may have important implications for clinical use of GL-II-73, as periods of high hippocampal activity appear to favor synaptic α5GABAARs, thus efficacy may be diminished in conditions where aberrant hippocampal activity is present.Significance StatementDopamine activity is known to be altered in both psychosis patients and in animal models, with promising new antipsychotics restoring normal dopamine system function. One such drug is GL-II-73, a positive allosteric modulator of α5GABAARs (α5-PAM). Interestingly, previous research has shown that a positive allosteric modulator of α1GABAARs (α1-PAM) does not share this ability, even when directly given to the ventral hippocampus, a region known to modulate dopamine activity. One potential explanation for this difference we examined in this study is that α1GABAARs are primarily located in the synapse, whereas α5GABAARs are mostly extrasynaptic. Determining the mechanism of this differential efficacy could lead to the refinement of antipsychotic treatment and improve patient outcomes overall.
Relationship Between the P300 and Sequence Knowledge in a Changing Environment
Authors: Chou Ko-Ping , Hsu Tzu-Yu 
Published: July 2023

AbstractThe P300 amplitude has been linked to the processing of uncertain events. Studies have assumed that knowledge extracted from sequences of events corresponds to event probability. The relationship between the P300 and event uncertainty has been studied using the model-based analysis, in which the subjective expectancy of event probability is modeled and examined by using a quantity called “surprise.” However, other types of sequence knowledge exist, such as event transition probabilities, which comprises both event repetitions and event alterations. Whether the state of the environment affects the encoded sequence knowledge is not fully understood, and the type of sequence knowledge, event probability or event transition probability, that is encoded in the brain in a changing environment remains unknown. We determined whether fluctuations in the P300 are better explained by surprise based on a model of event probability or by surprise based on a model of event transition probability. Participants completed a two-choice response task in which a binary sequence was generated from a hidden Markov model. Reaction times indicated that behavior changed depending on the event transitions. The model-based analysis revealed that trial-by-trial P300 was better explained by surprise based on a model of event transition probability. Our results suggest that humans use the sequence knowledge of event transitions in a changing environment.
Snapshots of ribosome dynamics near atomic-resolution in situ: full insight into the eukaryotic elongation cycle
Authors: Cheng Jing , Wu Chunling , Li Junxi , Yang Qi , Zhao Mingjie , Zhang Xinzheng 
Published: July 2023

AbstractMany protein complexes are highly dynamic in cells, characterizing their conformational changes in cells is crucial for unraveling their functions. In this report, using cryo-electron microscopy, 451,700 ribosome particles fromSaccharomyces cerevisiaecell lamellae were obtained to solve the 60S region to 2.9 Å resolution by in situ single particle analysis. Over 20 distinct conformations were identified by 3D classification with resolutions typically higher than 4 Å. These conformations were used to reconstruct a complete elongation cycle of eukaryotic translation with elongation factors. We found that compact eEF2 anchors to the partially rotated ribosome after subunit rolling, and hypothesize that it stabilizes the local conformation for peptidyl transfer. Moreover, an open eEF3 binding to a fully rotated ribosome was observed, whose conformational change was coupled with head swiveling and body back-rotation of the 40S subunit.
Bark traits affect epiphytic bryophyte community assembly in a temperate forest
Authors: Tatsumi Shinichi , Ohgue Takayuki , Azuma Wakana A. , Nishizawa Keita 
Published: July 2023

AbstractBark traits of trees often serve as a key factor determining the community structure of epiphytes. However, the extent to which barks modulate the relative importance of abiotic and biotic assembly processes of epiphytes is poorly understood. Here, using a community phylogenetic approach, we aimed to infer the assembly processes of epiphytic mosses and liverworts on tree species with varying bark traits in a temperate forest of central Japan. We observed a total of 56 moss and 35 liverwort species on 150 trees. Moss communities showed decreasing species richness and a tendency toward phylogenetic overdispersion, that is, higher phylogenetic diversity than expected by chance, in relation to increasing bark roughness, acidity, and wetness. Along the same bark gradients, liverwort communities became phylogenetically clustered. Species richness of both mosses and liverworts increased with the nitrogen content of barks. The results indicate non-random assembly processes such as interspecific competition on resource-rich barks and abiotic filtering associated with environmental harshness and microhabitat variety determined by barks. Our findings imply that bark traits modulate community assembly processes through which epiphyte diversity is maintained.
Is using Dual Energy Virtual Enhancing over Non-Contrast CT beneficial in terms of Diagnostic Accuracy of finding Adrenal Adenoma? : A Meta-analysis
Authors: Desai Dev , Duisenbayev Arman , Maniyar Pankti , Malafi Maria Eleni , Andharia Dev , Shah Abhijay B. 
Published: July 2023

AbstractBackgroundThe study compared the diagnostic accuracy of Dual Energy Virtual Non-Contrast CT (DEvNCT) to Non-Contrast CT (NCT) for adrenal adenomas. Adrenal nodules on CT scans require precise characterization to differentiate between benign and malignant lesions. CT imaging uses features like low attenuation and contrast enhancement to identify adenomas. However, distinguishing adenomas from non-adenoma lesions can be challenging due to overlapping attenuation levels.DEvNCT, a post-processing technique enabled by dual-energy CT, optimizes adrenal lesion evaluation. The study aimed to compare the diagnostic accuracy of DEvNCT and NCT for adrenal adenomas.MethodologyA systematic review and meta-analysis searched relevant literature in PubMed, Google Scholar, and Cochrane Library databases. The analysis included nine randomized controlled trials (RCTs) with 407 patients: three RCTs for NCT vs. Biopsy and six RCTs for DEvNCT vs. NCT. Study quality was assessed using appropriate tools.ResultResults revealed DEvNCT had 72% sensitivity, 94% specificity, and 0.878 positive predictive value for adrenal adenoma diagnosis. NCT had 80% sensitivity, 68.1% specificity, and 0.831 positive predictive values. The difference in specificity between DEvNCT and NCT was significant, indicating DEvNCT’s superior ability to identify adenomas accurately.ConclusionThe study concluded that DEvNCT exhibited comparable sensitivity but higher specificity than NCT in diagnosing adrenal adenomas. DEvNCT could potentially reduce follow-up imaging, lower costs, and minimize radiation exposure. However, biopsy remains the gold standard for confirming adrenal adenoma diagnosis.Overall, DEvNCT shows promise for improving diagnostic accuracy compared to NCT in diagnosing adrenal adenomas. Further research and clinical validation are needed to confirm these findings.
Molecular mechanism of acid stress response ofA. acidoterrestrisDSM 3922Tunder sublethal pH environment
Authors: Liu Xiaoxue , Wu Youzhi , Jiao Lingxia , Ran Junjian , Sun Linjun , Ye Fuzhou , Liang Xinhong , Zhao Ruixiang 
Published: July 2023

AbstractAcid-responsive proteome expression profiles ofAlicyclobacillus acidoterrestris(A. acidoterrestris) were analysed using label-free quantitative mass spectrometry to investigate its acid resistance mechanism at sublethal pH. Totally, 325 differential expression proteins were identified during acid stress at pH2.5 condition for 15 min, of which the expressions of 83 proteins were up-regulated and the other 242 proteins expressions were down-regulated. Differentially expressed proteins were mainly involved in organic nitrogen compounds metabolism, small molecule metabolism, organic acid metabolism and signal transduction. Overall, they were mapped into 97 metabolic pathways. Combination of KEGG pathway analysis and protein functional analysis suggested that the pH homeostasis system, changes in metabolic pathways, cell membrane permeability and DNA repair are the main acid resistance mechanisms ofA. acidoterrestrisat sublethal pH conditions. It is speculated thatA. acidoterrestrismay sense and transmit pH signals from the external environment through the nhaB protein which holds histidine-dependent acid resistance system, initiating a series of acid tolerance reactions. Our study demonstrated global physiological response ofA. acidoterrestristo sublethal pH, which provided a better understanding of acid adaption mechanism ofA. acidoterrestris.
Analysis of a European general wildlife health surveillance program: chances, challenges and recommendations
Authors: Heiderich Elisabeth , Keller Saskia , Pewsner Mirjam , Origgi Francesco Carlo , Zürcher-Giovannini Samoa , Borel Stéphanie , Marti Iris , Scherrer Patrick , Pisano Simone Roberto Rolando , Friker Brian , Adrian-Kalchhauser Irene , Ryser-Degiorgis Marie-Pierre 
Published: July 2023

AbstractIn the context of a One Health perspective general wildlife health surveillance (GWHS) gains importance worldwide, as pathogen transmission among wildlife, domestic animals and humans raises health, conservation and economic concerns. However, GWHS programs operate in the face of legal, geographical, financial, or administrative conditions. The present study uses a multi-tiered approach to understand the current characteristics, strengths and gaps of a European GWHS that operates in a fragmented legislative and multi-stakeholder environment. The aim is to support the implementation or improvement of other GWHS systems by managers, surveillance experts, and administrations.To assess the current state of wildlife health investigations and trends within the GWHS, we analyzed 20 years of wildlife diagnostic data, conducted an online survey and phone interviews with official field partners (hunting administrators, game wardens and hunters), and performed a time-per-task analysis.Firstly, we found that infectious disease dynamics, the level of public awareness for specific diseases, research activities and increasing population sizes of in depth-monitored protected species, together with biogeographical and political boundaries all impacted case numbers and can present unexpected challenges to a GWHS. Secondly, we found that even a seemingly comprehensive GWHS can feature pronounced information gaps, with underrepresentation of common or easily recognizable diseases, blind spots in non-hunted species and only a fraction of discovered carcasses being submitted. Thirdly, we found that substantial amounts of wildlife health data may be available at local hunting administrations or disease specialist centers, but outside the reach of the GWHS and its processes.In conclusion, we recommend that fragmented and federalist GWHS programs like the one addressed require a central, consistent and accessible collection of wildlife health data. Also, considering the growing role of citizen observers in environmental research, we recommend using online reporting systems to harness decentrally available information and fill wildlife health information gaps.