bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Diagnostic Performance of urine dipstick test for Detection of urinary tract infections in patients treated in Kenyan hospitals.
Authors: Maina John , Mwaniki John , Mwiti Franklin , Kiiru Susan , Katana Japhet , Wanja Fredrick , Mukaya Joel , Khasabuli Osborn , Kiiru John 
Published: August 2022

Introduction
Culture is the gold-standard diagnosis for Urinary Tract Infections (UTIs). However, most hospitals in poor-resource countries lack adequately equipped laboratories and relevant expertise to perform culture and therefore heavily rely on dipstick tests as an alternative diagnostic method for UTIs.
Research gap
In many Kenyan hospitals, routine evaluations are rarely done to assess the reliability of popular screening tests such as the dipstick test. As such, there is a high risk of misdiagnosis emanating from inappropriate or insufficient use of proxy screening tests over the goal standards. As a result, this may lead to misuse, under-use, or over-use of antimicrobials and treatment failure.
Aim
The present study sought to assess the reliability of the urine dipstick test as a proxy for the diagnosis of urinary tract infections in selected Kenyan hospitals.
Results
Using a cross-sectional hospital-based approach, the present study evaluated the performance of urine dipstick test in UTI diagnosis using culture as the gold standard. A UTI prevalence of 54.1% was found using culture. This was lower than the 66.4% recorded by the dipstick test. Estimated UTI prevalence by Nitrate test, RBCs, and Leukocyte's esterase (L.E) was 11.9%, 28.1 %, and 46%, which were lower than the observed. The nitrate test had a sensitivity of 19.8%, which was lower than 32.9%, 65.5%, and 66.2% by RBCs, all dipstick parameters, and L.E, respectively. Nitrate test (97.4%) and RBCs (77.6%) had a better specificity compared to L.E (56.5%) and all dipstick parameters combined (68.3%).
Conclusion
The prevalence discrepancies from the observed and low sensitivity and Specificity imply dipstick test inadequacy for accurate UTI diagnosis. The finding also demonstrates the need for urine culture for accurate UTI diagnosis.
Epigenetic memory acquired during long-term EMT induction governs the recovery to the epithelial state
Authors: Jain Paras , Corbo Sophia , Mohammad Kulsoom , George Jason T , Levine Herbert , Toneff Michael , Jolly Mohit Kumar 
Published: August 2022

AbstractEpithelial-Mesenchymal Transition (EMT) and its reverse Mesenchymal-Epithelial Transition (MET) are critical during embryonic development, wound healing and cancer metastasis. While phenotypic changes during short-term EMT induction are reversible, long-term EMT induction has been often associated with irreversibility. Here, we show that phenotypic changes seen in MCF10A cells upon long-term EMT induction by TGFβ need not be irreversible, but have relatively longer timescales of reversibility than those seen in short-term induction. Next, using a phenomenological mathematical model incorporating the epigenetic silencing of miR-200 by ZEB, we highlight how the epigenetic memory gained during long-term EMT induction can slow the recovery to the epithelial state post-TGFβ withdrawal. Our results suggest that epigenetic modifiers can govern the extent and timescale of EMT reversibility, and advise caution against labelling phenotypic changes seen in long-term EMT induction as ‘irreversible’.
A dynamic sequence of visual processing initiated by gaze shifts
Authors: Parker Philip R. L. , Martins Dylan M. , Leonard Emmalyn S. P. , Casey Nathan M. , Sharp Shelby L. , Abe Elliott T. T. , Smear Matthew C. , Yates Jacob L. , Mitchell Jude F. , Niell Cristopher M. 
Published: August 2022

AbstractAnimals move their head and eyes as they explore and sample the visual scene. Previous studies have demonstrated neural correlates of head and eye movements in rodent primary visual cortex (V1), but the sources and computational roles of these signals are unclear. We addressed this by combining measurement of head and eye movements with high density neural recordings in freely moving mice. V1 neurons responded primarily to gaze shifts, where head movements are accompanied by saccadic eye movements, but not to head movements where compensatory eye movements stabilize gaze. A variety of activity patterns immediately followed gaze shifts, including units with positive, biphasic, or negative responses, and together these responses formed a temporal sequence following the gaze shift. These responses were greatly diminished in the dark for the vast majority of units, replaced by a uniform suppression of activity, and were similar to those evoked by sequentially flashed stimuli in head-fixed conditions, suggesting that gaze shift transients represent the temporal response to the rapid onset of new visual input. Notably, neurons responded in a sequence that matches their spatial frequency preference, from low to high spatial frequency tuning, consistent with coarse-to-fine processing of the visual scene following each gaze shift. Recordings in foveal V1 of freely gazing head-fixed marmosets revealed a similar sequence of temporal response following a saccade, as well as the progression of spatial frequency tuning. Together, our results demonstrate that active vision in both mice and marmosets consists of a dynamic temporal sequence of neural activity associated with visual sampling.HighlightsDuring free movement, neurons in mouse V1 respond to head movements that are accompanied by a gaze-shifting saccadic eye movement, but not a compensatory eye movement.Neurons respond to gaze shifts with diverse temporal dynamics that form a sequence across the population, from early positive responses to biphasic and negative responses.In darkness, most neurons show a uniform suppression following a gaze shift.Temporal dynamics of responses correspond to a neuron’s temporal and spatial frequency preferences, consistent with a coarse-to-fine processing sequence.A similar temporal sequence following saccades is observed in foveal V1 of freely gazing head-fixed marmosets, demonstrating shared aspects of active visual processing across species.
The impact of maternal dietary folic acid or choline deficiencies on cerebral blood flow, cardiac, aortic, and coronary function in young and middle-aged female mouse offspring following ischemic stroke
Authors: Pull Kasey , Folk Robert , Kang Jeemin , Jackson Shaley , Gusek Brikena , Esfandiarei Mitra , Jadavji Nafisa M. 
Published: August 2022

AbstractBackground and PurposeAdequate maternal dietary levels of one-carbon (1C) metabolites, such as folic acid and choline, play an important role in the closure of the neural tubein utero; however, the impact of deficiencies in 1C on offspring neurological function after birth remain undefined. Stroke is one of the leading causes of death and disability globally. The aim of our study was to determine the impact of maternal 1C nutritional deficiencies on cerebral and peripheral blood flow after ischemic stroke in adult female offspring.MethodIn this study, female mice were placed on either control (CD), folic acid (FADD), or choline (ChDD) deficient diets prior to pregnancy. Female offspring were weaned onto a CD for the duration of the study. Ischemic stroke was induced in offspring and after six weeks cerebral and peripheral blood flow velocity was measured using ultrasound imaging.ResultsOur data showed that 11.5-month-old female offspring from ChDD mothers had reduced blood flow in the posterior cerebral artery compared to controls. In peripheral blood flow velocity measurements, we report an aging effect.ConclusionsThese results emphasize the importance of maternal 1C diet in early life neuro-programming on long-term vasculature health.
Co-infection of Ehrlichia with B. burgdorferi drives emergency myelopoiesis and promotes Lyme arthritis
Authors: Bonin Jesse L. , Torres Steven R. , Marcinkiewicz Ashley L. , Yang Xiuli , Pal Utpal , DiSpirito Julia M. , Nowak Tristan , Lin Yi-Pin , MacNamara Katherine C. 
Published: August 2022

AbstractLyme disease is caused by the extracellular pathogen Borrelia burgdorferi (Bb), transmitted by the Ixodes scapularis tick. Approximately one-third of infected individuals develop arthritis of weight-bearing joints, though it is unclear why some patients develop arthritis and severe systemic disease while others do not. C57BL/6 (B6) mice are susceptible to Bb infection but do not develop arthritis, providing an in vivo model to evaluate mechanisms regulating development of Lyme arthritis. We demonstrate here that co-infection of B6 mice with the tick-borne pathogens Bb and Ehrlichia muris (Em) induced significant arthritis. Although co-infection did not impact bacterial burden or growth of either pathogen, the resultant Lyme arthritis in co-infected mice correlated with significant hematologic disturbances. Whereas single Bb infection elicited no overt hematologic changes, Em infection resulted in thrombocytopenia, lymphopenia, monocytosis, and granulocytosis, which was consistently observed in mice co-infected with both Bb and Em. Hematologic changes correlated with profound changes to the hematopoietic stem and progenitor cell (HSPC) populations in Em-infected mice. Most notable were dramatic reductions in populations of HSPCs committed to myeloid-biased differentiation. Co-infection resulted in persistent hematologic changes and bone marrow inflammation. Our data demonstrate for the first time that B6 mice, resistant to developing Lyme arthritis, exhibit severe joint pathology in the presence of a second pathogen, correlating with persistent emergency myelopoiesis. Our data support the conclusion that pathogen burden is not sufficient for disease and specific inflammatory signals and cells regulate the development of Lyme arthritis.ImportanceTick-borne illnesses, historically relegated to specific geographic areas, are increasing in prevalence and distribution. Borrelia burgdorferi causes Lyme disease, the most common tick-borne illness in North America, characterized by debilitating arthritis, carditis, and neurologic complications. It remains unclear why certain infected individuals develop severe disease while others are only mildly symptomatic. Human monocytic ehrlichiosis (HME) is another tick-borne disease that often results in profound illness and severe hematological disturbances. We show here that co-infection of B6 mice, resistant to Lyme arthritis, with Borrelia burgdorferi and Ehrlichia muris, used to model HME, results in the development of severe arthritis and emergency myelopoiesis. Our work suggests that immune activation driven by co-infection contributes to the development of Lyme arthritis.
Identification of 64 new risk loci for major depression, refinement of the genetic architecture and risk prediction of recurrence and comorbidities
Authors: Als Thomas D. , Kurki Mitja , Grove Jakob , Voloudakis Georgios , Therrien Karen , Tasanko Elisa , Nielsen Trine Tollerup , Naamanka Joonas , Veerapen Kumar , Levey Daniel , Bendl Jaroslav , Bybjerg-Grauholm Jonas , Zheng Biao , Demontis Ditte , Rosengren Anders , Athanasiadis Georgios , Bækved-Hansen Marie , Qvist Per , Walters Bragi , Thorgeirsson Thorgeir , Stefánsson Hreinn , Musliner Katherine L , Manikandan Veera , Farajzadeh Leila , Thirstrup Janne , Vilhjálmsson Bjarni J. , McGrath John J. , Mattheisen Manuel , Meier Sandra ,   iPSYCH-Broad Consortium, Agerbo Esben , Stefánsson Kári , Nordentoft Merete , Werge Thomas , Hougaard David M. , Mortensen Preben B. , Stein Murray , Gelernter Joel , Hovatta Iiris , Roussos Panos , Daly Mark J. , Mors Ole , Palotie Aarno , Børglum Anders D. 
Published: August 2022

AbstractMajor depression (MD) is a common mental disorder and a leading cause of disability worldwide. We conducted a GWAS meta-analysis of more than 1.3 million individuals, including 371,184 with MD, identifying 243 risk loci. Sixty-four loci are novel, including glutamate and GABA receptors that are targets for antidepressant drugs. Several biological pathways and components were enriched for genetic MD risk, implicating neuronal development and function. Intersection with functional genomics data prioritized likely causal genes and revealed novel enrichment of prenatal GABAergic neurons, astrocytes and oligodendrocyte lineages.We found MD to be highly polygenic, with around 11,700 variants explaining 90% of the SNP heritability. Bivariate Gaussian mixture modeling estimated that > 97% of risk variants for other psychiatric disorders (anxiety, schizophrenia, bipolar disorder and ADHD) are influencing MD risk when both concordant and discordant variants are considered, and nearly all MD risk variants influence educational attainment. Additionally, we demonstrated that MD genetic risk is associated with impaired complex cognition, including verbal reasoning, attention, abstraction and mental flexibility.Analyzing Danish nation-wide longitudinal data, we dissected the genetic and clinical heterogeneity, revealing distinct polygenic architectures across case subgroups of MD recurrency and psychiatric comorbidity and demonstrating two-to six-fold increases in absolute risks for developing comorbid psychiatric disorders among MD cases with the highest versus the lowest polygenic burden.The results deepen the understanding of the biology underlying MD and its progression and inform precision medicine approaches in MD.
An accessible and versatile deep learning-based sleep stage classifier
Authors: Hanna Jevri , Flöel Agnes 
Published: August 2022

AbstractManual sleep analysis for research purposes and for the diagnosis of sleep disorders is labor-intensive and often produces unreliable results, which has motivated many attempts to design automatic sleep stage classifiers. With the recent introduction of large, publicly available hand-scored polysomnographic data, and concomitant advances in machine learning methods to solve complex classification problems with supervised learning, the problem has received new attention, and a number of new classifiers that provide excellent accuracy. Most of these however have non-trivial barriers to use. We introduce the Greifswald Sleep Stage Classifier (GSSC), which is free, open source, and can be relatively easily installed and used on any moderately powered computer. In addition, the GSSC has been trained to perform well on a large variety of electrode set-ups, allowing high performance sleep staging with portable systems. The GSSC can also be readily integrated into brain-computer interfaces for real-time inference. These innovations were achieved while simultaneously reaching a level of accuracy equal to, or exceeding, recent state of the art classifiers and human experts, making the GSSC an excellent choice for researchers in need of reliable, automatic sleep staging.
Single-nuclear RNA sequencing of endomyocardial biopsies identifies persistence of donor-recipient chimerism with distinct signatures in severe cardiac allograft vasculopathy
Authors: Amancherla Kaushik , Qin Juan , Hulke Michelle L , Pfeiffer Ryan D , Agrawal Vineet , Sheng Quanhu , Xu Yaomin , Schlendorf Kelly H , Lindenfeld JoAnn , Shah Ravi V , Freedman Jane E , Tucker Nathan R , Moslehi Javid 
Published: August 2022

ABSTRACTCardiac allograft vasculopathy (CAV) is the leading cause of late allograft failure and mortality after heart transplantation. As current standards of diagnosis and treatment of CAV have significant limitations, understanding cell-specific responses may prove critical for developing improved detection strategies and novel therapeutics. This study is the first to successfully utilize human endomyocardial biopsy (EMB) samples to isolate large numbers of intact nuclei for single-nuclear transcriptomics. These data also lay the groundwork for ongoing experiments to study serial, routinely-collected EMB specimens after heart transplantation to identify novel biomarkers and pathways through which early CAV pathogenesis can be interrupted, thereby prolonging allograft survival.
HepaCAM Suppresses Glioblastoma Stem Cell Invasion in the Brain
Authors: De Arpan , Lattier John M. , Morales John E. , Kelly Jack R. , Zheng Xiaofeng , Chen Zhihua , Sebastian Sumod , Huse Jason T. , Lang Frederick F. , McCarty Joseph H. 
Published: August 2022

AbstractGlioblastoma (GBM) is a malignant brain cancer that contains sub-populations of highly invasive tumor cells that drive progression and recurrence after surgery and radiochemotherapy. The exact mechanisms that enable GBM cells to disperse from the main tumor mass and navigate throughout the brain microenvironment remain largely unknown. As a result, there is a lack of effective strategies to block cancer cell invasive growth in primary and recurrent GBM. Here we report that hepatocyte cell adhesion molecule (hepaCAM), which is normally expressed in perivascular astrocytes, plays central roles in controlling the invasive growth features of GBM cells. Genetically targeting HEPACAM induces a transition from GBM cell proliferation/self-renewal to invasion. Increased invasion is due, in part, to an activation of focal adhesion signaling pathways and enhanced GBM cell adhesion to the extracellular matrix (ECM) in the brain microenvironment. Transcriptional profiling of GBM cells reveals various HEPACAM-regulated genes with links to polarity and invasion. Collectively, these data show that hepaCAM balances ECM adhesion and signaling pathways to control cancer cell proliferation versus invasion in the brain parenchyma. Targeting select components of the hepaCAM pathway may be an effective way to block tumor progression and recurrence in patients with GBM.
The effect of selective logging on microclimates, arthropod abundance and the foraging behaviour of Eastern Himalayan birds
Authors: Aggarwal Kanika , Chanda Ritobroto , Rai Shambu , Rai Mangal , Pradhan D.K. , Munda Binod , Tamang Bharat , Biswakarma Aman , Srinivasan Umesh 
Published: August 2022

ABSTRACT1. Selective logging—the practice of removing a subset of commercially important trees from a forest—is a globally pervasive form of forest degradation. Selective logging alters both the structure and function of forests and the composition of ecological communities.2. Tropical insectivorous birds are highly vulnerable to microhabitat alterations in logged forest. Such altered microhabitats might affect the foraging of forest birds by altering (a) resource availability, and (b) foraging behaviour.3. We investigated the effect of selective logging on microclimates, prey availability, foraging behaviour and the foraging success of eastern Himalayan birds in the breeding season.4. Selective logging alters temperature-humidity microclimates and the composition of arthropod communities, both of which are likely to then collectively alter foraging behaviour by birds. We show that birds spent a lower proportion of their time foraging in primary compared with logged forest. Further, selective logging interacts with species traits such as body mass, preferred foraging stratum (understorey, midstorey or canopy) and foraging manoeuvre to influence foraging success. Gleaners generally foraged more successfully in primary forest and salliers in logged forest, although these patterns were modified by body mass and foraging stratum.5. Synthesis and applications: Our study shows how altered microclimates in anthropogenically modified habitats can influence resource availability and have downstream impacts on the behaviour of species at higher trophic levels.
Antimicrobial peptides do not directly contribute to aging inDrosophila, but improve lifespan by preventing dysbiosis
Authors: Hanson M.A. , Lemaitre B. 
Published: August 2022

AbstractAntimicrobial peptides (AMPs) are innate immune effectors first studied for their role in host defense against bacterial and fungal infections. Recent studies have implicated these peptides in the clearance of aberrant cells and various neurological processes including neurodegenerative syndromes. InDrosophila, an array of AMPs are produced downstream of the Toll and Imd NF-κB pathways in response to infection. Many studies have suggested a role for the Imd pathway and AMPs in aging in this insect, supported by the upregulation of AMPs with aging (so-called “inflammaging”). However, functional studies using RNAi or over-expression have been inconclusive on whether and how these immune effectors impact aging.Leveraging a new set of single and compound AMP gene deletions in a controlled genetic background, we have investigated how AMPs contribute to aging. Overall, we found no major effect of individual AMPs on lifespan, with a possible exception ofDefensin. However,ΔAMP14flies lacking 14 AMP genes from seven families display a reduced lifespan. Interestingly, we found an increased bacterial load in the food medium of agedΔAMP14flies, suggesting that the lifespan reduction of these flies was due to a failure in controlling the microbiome. Consistent with this idea, use of germ-free conditions extends the lifespan ofΔAMP14flies. Overall, our results do not point to an overt role of individual AMPs in lifespan. Instead, we find that AMPs collectively impact lifespan by preventing dysbiosis over aging. This is consistent with our previous study showing that AMPs control the gut microbiome, and many works showing that dysbiosis is detrimental upon aging. In the course of our experiments, we also uncovered a strong impact of aDrosophila nora virusinfection on lifespan, and share our experience in reconciling our data given this confounding cryptic factor.
Zika virus-induces metabolic alterations in fetal neuronal progenitors that could influence in neurodevelopment during early pregnancy
Authors: Gilbert-Jaramillo Javier , Purnama Ujang , Molnár Zoltán , James William S. 
Published: August 2022

AbstractNeuronal progenitor subtypes have distinct fate restrictions regulated by time-dependent activation of energetic pathways. Thus, the hijacking of cellular metabolism by Zika virus (ZIKV) to support its replication may contribute to damage in the developing fetal brain. Here, we showed that ZIKV replicates differently in two glycolytically distinct hiPSC-derived neuronal progenitors that correspond to early and late progenitors in the forebrain. This differential replication alters the transcription of metabolic genes and upregulates the glycolytic capacity of progenitor subtypes. Analysis using Imagestream® revealed that, during early stages of infection, ZIKV replication in early progenitors increases lipid droplet abundance and decreases mitochondrial size and membrane potential. During later stages infection, early progenitors show increased subcellular distribution of lipid droplets, whilst late progenitors show decreased mitochondria size. The finding that there are hi-NPC subtype-specific alterations of cellular metabolism during ZIKV infection may help to explain the differences in brain damage over each trimester.