bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human neurons lacking amyloid precursor protein exhibit cholesterol-associated developmental and presynaptic deficits
Authors: Mesa Haylee , Zhang Elaine Y. , Wang Yingcai , Zhang Qi 
Published: December 2022

AbstractAmyloid precursor protein (APP) produces aggregable β-amyloid peptides and its mutations are associated with familial Alzheimer’s disease, which makes it one of the most studied proteins. However, APP’s role in the human brain remains unclear despite years of investigation. One problem is that most studies on APP have been carried out in cell lines or model organisms, which are physiologically different from human neurons in the brain. Recently, human induced neurons (hiNs) derived from induced pluripotent stem cells provide a practical platform for studying the human brainin vitro. Here, we generated APP-null iPSCs using CRISPR/Cas9 genome editing technology and differentiate them to matured human neurons with functional synapses using a two-step procedure. During hiN differentiation and maturation, APP-null cells exhibited less neurite growth and reduced synaptogenesis in serum-free but not serum-containing media. We have found that cholesterol (Chol) remedies those developmental defects in APP-null cells, consistent with Chol’s role in neurodevelopment and synaptogenesis. Phenotypic rescue was also achieved by co-culturing those cells with wildtype mouse astrocytes, suggesting that APP’s developmental role is likely astrocytic. Next, we examined matured hiNs using patch-clamp recording and detected reduced synaptic transmission in APP-null cells. This change was largely due to decreased synaptic vesicle (SV) release and retrieval, which was confirmed by live-cell imaging using two SV-specific fluorescent reporters. Adding Chol shortly before stimulation mitigated the SV deficits in APP-null iNs, indicating that APP facilitates presynaptic membrane Chol turnover during SV exo-/endocytosis cycle. Taken together, our study in hiNs supports the notion that APP contributes to neurodevelopment, synaptogenesis and neurotransmission via maintaining brain Chol homeostasis. Given the vital role of Chol in the central nervous system, the functional connection between APP and Chol bears important implication in the pathogenesis of Alzheimer’s disease.
Estimates of COVID-19 deaths in Mainland China after abandoning zero COVID policy
Authors: Ioannidis John P.A. , Zonta Francesco , Levitt Michael 
Published: December 2022

ABSTRACTBackgroundChina witnessed a surge of Omicron infections after abandoning zero COVID strategies on December 7, 2022. The authorities report very sparse deaths based on very restricted criteria, but massive deaths are speculated.MethodsWe aimed to estimate the COVID-19 fatalities in Mainland China until summer 2023 using the experiences of Hong Kong and of South Korea in 2022 as prototypes. Both these locations experienced massive Omicron waves after having had very few SARS-CoV-2 infections during 2020-2021. We estimated age-stratified infection fatality rates (IFRs) in Hong Kong and South Korea during 2022 and extrapolated to the population age structure of Mainland China. We also accounted separately for deaths of residents in long-term care facilities in both Hong Kong and South Korea.ResultsIFR estimates in non-elderly strata were modestly higher in Hong Kong than South Korea and projected 987,455 and 619,549 maximal COVID-19 deaths, respectively, if the entire China population was infected. Expected COVID-19 deaths in Mainland China until summer 2023 ranged from 49,962 to 691,219 assuming 25-70% of the non-elderly population being infected and variable protection of elderly (from none to three-quarter reduction in fatalities). The main analysis (45% of non-elderly population infected and fatality impact among elderly reduced by half) estimated 152,886-249,094 COVID-19 deaths until summer 2023. Large uncertainties exist regarding potential changes in dominant variant, health system strain, and impact on non-COVID-19 deaths.ConclusionsThe most critical factor that can affect total COVID-19 fatalities in China is the extent to which the elderly can be protected.
DNA origami 2.0
Authors: Agarwal Nayan P. , Gopinath Ashwin 
Published: December 2022

AbstractDNA origami is a technique that allows the creation of precise, modular, and programmable nanostructures using DNA. These nanostructures have found use in several fields like biophysics, molecular biology, nanoelectronics, and nanophotonic due to their programmable nature as well as ability to organize other nanomaterials with high accuracy. However, they are fragile and unstable when removed from their optimal aqueous conditions. In contrast, other commonly used bottom-up methods for creating inorganic nanoparticles do not have these issues, but it is difficult to control the shape or spatial organization of ligands on these nanoparticles. In this study, we present a simple, highly controlled method for templated growth of silica on top of DNA origami while preserving all the salient features of DNA origami. Using the polyplex micellization (PM) strategy, we create DNA nanostructures that can withstand salt-free, buffer-free, alcohol-water mixtures, enabling us to control the material growth conditions while maintaining the monodispersity and organization of nanoelements. We demonstrate the growth of silica shells of different thicknesses on brick and ring-shaped DNA origami structures using the standard Stöber process. We also demonstrate the thermostability of the silica-coated nanostructures as well as accessibility of surface sites programmed into the DNA origami after the silica growth in the final inorganic nanostructure.
Atypical B cells mediate poor response to Bacillus Calmette Guérin immunotherapy in non-muscle invasive bladder cancer
Authors: Yolmo Priyanka , Rahimi Sadaf , Chenard Stephen , Conseil Gwenaëlle , Jenkins Danielle , Sachdeva Kartik , Emon Isaac , Hamilton Jake , Xu Minqi , Rangachari Manu , Michaud Eva , Mansure Jose , Kassouf Wassim , Berman David M. , Siemens D. Robert , Koti Madhuri 
Published: December 2022

AbstractPoor response to Bacillus Calmette-Guérin (BCG) immunotherapy remains a major barrier in the management of patients with non-muscle-invasive bladder cancer (NMIBC). Among the multiple factors contributing to poor outcomes, a B cell infiltrated pre-treatment immune microenvironment of NMIBC tumors has emerged as a key determinant of response to BCG. The mechanisms underlying the paradoxical roles of B cells in NMIBC are poorly understood. Here, we show that B cell dominant tertiary lymphoid structures (TLSs), a hallmark feature of chronic mucosal immune response, are abundant and located close to the epithelial compartment in pre-treatment tumors from BCG non-responders. Digital spatial proteomic profiling of whole tumor sections revealed higher expression of immune exhaustion-associated proteins within the TLSs from both responders and non-responders. Chronic local inflammation, induced by the N-butyl- N-(4-hydroxybutyl) nitrosamine (BBN) carcinogen, led to TLS formation with recruitment and differentiation of the immunosuppressive atypical B cell (ABCs) subset within the bladder microenvironment, predominantly in aging female mice compared to their male counterparts. Depletion of ABCs simultaneous to BCG treatment delayed cancer progression in female mice. Our findings provide the first evidence indicating the role of ABCs in BCG response and will inform future development of therapies targeting the B cell exhaustion axis.
An Autoinhibited Conformation of the DnaB-Replicative Helicase – phage λP Helicase Loader Complex
Authors: Brown Dhanjai , Shatarupa Abhipsa , Olinares Paul Dominic B. , Chase Jillian , Isiorho Eta , Chait Brian T. , Jeruzalmi David 
Published: December 2022

AbstractReplicative helicases require loader proteins for assembly at origins of DNA replication. Multiple copies of the bacteriophage λP loader bind to theE. coliDnaB replicative helicase and trigger its reconfiguration into a right-handed open spiral wherein an internal chamber becomes accessible to physiological single stranded DNA. In the 2.84 Å model of the DnaB – λP complex, the pentameric λP ensemble adopts an asymmetric configuration; one copy of λP, which is visualized in full, binds at the top and bottom of the open DnaB spiral; the presence of a single breach in the DnaB open spiral implies that the remaining four copies of λP must adopt distinct conformations. DnaB’s internal chamber remains accessible to ssDNA, however, the λP protomer whose binding site spans the breach effectively blocks the path into the inner chamber to give rise to an autoinhibited configuration for the complex. Although the path to the inner chamber is blocked, the BP complex, nevertheless, binds ssDNA, and we suggest that the path for ssDNA lies outside the DnaB ring. Comparisons of the λP and DnaC complexes of the DnaB helicase shed new light on how the two loaders, though unrelated in structure, converged on the same ring-opening mechanism. Our structure suggests the conformation changes that accompany recruitment to the initiator protein complex at the replication origin.Graphical AbstractThe autoinhibited configuration of the DnaB helicase λP loader complex. Interaction with the loader reconfigures the helicase, depicted in the ribbon format and under a transparent surface, into an open spiral, with its internal chamber exposed to solvent. One copy of the λP loader binds across the single breached interface in DnaB, effectively blocking the path into the inner chamber. The pink cylinder represents the expected path of ssDNA through DnaB.
Self-pressurized rapid freezing at arbitrary cryoprotectant concentrations
Authors: Rolle K. , Okotrub K.A. , Zaytseva I.V. , Babin S.A. , Surovtsev N.V. 
Published: December 2022

ABSTRACTSelf-pressurized rapid freezing (SPRF) has been proposed as a simple alternative to traditional high pressure freezing (HPF) protocols for vitrification of biological samples in electron microscopy and cryopreservation applications. Both methods exploit the circumstance that the melting point of ice reaches a minimum when subjected to pressure of around 210 [MPa], however, in SPRF its precise quantity depends on sample properties and hence, is generally unknown. In particular, cryoprotective agents (CPAs) are expected to be a factor; though eschewed by many SPRF experiments, vitrification of larger samples notably cannot be envisaged without them. Thus, in this study, we address the question of how CPA concentration affects pressure inside sealed capillaries, and how to design SPRF experiments accordingly. By embedding a fiber-optic probe in samples and performing Raman spectroscopy after freezing, we first present a direct assessment of pressure buildup during SPRF, enabled by the large pressure sensitivity of the Raman shift of hexagonal ice. Choosing dimethyl sulfoxide (DMSO) as a model CPA, this approach allows us to demonstrate that average pressure drops to zero when DMSO concentrations of 15 wt % are exceeded. Since a trade-off between pressure and DMSO concentration represents an impasse with regards to vitrification of larger samples, we introduce a sample architecture with two chambers, separated by a partition that allows for equilibration of pressure but not DMSO concentrations. We show that pressure and concentration in the fiber-facing chamber can be tuned independently, and present differential scanning calorimetry (DSC) data supporting the improved vitrification performance of two-chamber designs.
miR-17∼92 Suppresses Proliferation and Invasion of Cervical Cancer Cells by Inhibiting Cell Cycle Regulator Cdt2
Authors: Singh Garima , Sharma Sonika Kumari , Aastha  , Singh Samarendra Kumar 
Published: December 2022

AbstractCervical cancer (CC) is 4thlargest killer of women worldwide when diagnosed in late stages the treatment options are almost negligible. 99% of CC is caused by high risk human papilloma viruses (HR-HPV). Upon integration into human genome the encoded viral proteins mis-regulates various onco-suppressor and checkpoint factors including cell cycle regulators. One such factor is cell cycle S phase licensing factor Cdt2, which has been reported to be highly upregulated in various cancers including CC. HPV proteins also suppress several tumor suppressor miRNAs concluding miR-17-92 cluster. In this study we report that miR-17-92 directly recruits to 3’UTR of Cdt2 and downregulates this oncogene which suppresses the proliferation, migration, invasion capabilities of the CC cell lines while normal cells are fine. Suppression of Cdt2 by miR17-92 blocks the cancerous cells in S phase and induces apoptosis eventually leading to their death. Hence, our work for the first time mechanistically shows how miR17-92 could work as tumor suppressor opening up the potential of miR17-92 to be used in developing therapy for cervical cancer treatment.
A newly-recognized population of residual neural crest cells in the adult leptomeninges is re-activated for vascular repair
Authors: Nakamura Yoshihiko , Nakano Takafumi , Park Ji Hyun , Tanaka Masayoshi , Li Wenlu , Esposito Elga , Ahn Bum Ju , Durán-Laforet Violeta , Desai Rakhi , Sencan Ikbal , Sakadžić Sava , Lo Eng H. , Snyder Evan Y. , Tabaka Marcin , Hayakawa Kazuhide 
Published: December 2022

SummaryThe neural crest (NC) is a transient structure in vertebrate embryogenesis comprising highly migratory multipotent stem cells that give rise to a diverse array of cell types in organs throughout the body, including initiating neurovascular patterning. It is assumed that neural crest stem cells (NCSCs) disappear after development. Unexpectedly, using single-nucleus RNA-sequencing, we discovered residual quiescent NCSCs in the adult mouse meninges which are activated by injury and contribute to the brain’s homeostatic response. RNA velocity, pathway, and transcription factor analyses in a murine stroke model (combined with in vivo imaging) show that these adult NCSCs migrate towards the perivascular spaces of the infarct and undergo a perivascular stromal cell transition that is regulated by Ptp1b, Ghr, and Stat3. Loss- and gain-of-function experiments show that these “vestigial” NCSCs are required for restoring vascular endothelial barrier function via β-catenin and Stat3 signaling. These findings suggest that, in the adult, an unexpected reservoir of cells -- once pivotal to embryogenesis and vascular morphogenesis -- are re-invoked for neurovascular repair.
A model explaining environmental stiffness-dependent migration of fibroblasts with a focus on maturation of intracellular structures
Authors: Saito Natsuki , Matsui Tsubasa S , Matsunaga Daiki , Furukawa Kana , Deguchi Shinji 
Published: December 2022

AbstractCell migration is fundamental to many biological processes, while it remains elusive how cells modulate their migration upon different environmental stiffness. In this work, we focus on the structural maturity of actin stress fibers to explain the substrate stiffness-dependent emergence of different cell migration velocity. We demonstrate that fibroblasts migrate longer distances on softer elastic substrates, and the distance is increased by lowering the myosin-driven contractile force. Stress fibers, the major intracellular structure to generate and sustain contractile forces, were found to be less mature in structure on soft substrate than on stiff substrate. Based on these experimental results, we present a minimal mathematical model to capture the salient features of how the substrate stiffness alters the migration velocity. Specifically, the ability of cells to generate large contractile forces is limited on soft substrate according to the Hooke’s law. The inverse relationship between the cellular force and migration velocity is described by the Hill’s muscle equation. These mathematical descriptions suggest that the migration velocity is raised on softer substrate where cells exert a lower magnitude of contractile forces. Cells undergoing faster movement make stress fibers less mature in structure as mathematically described by the maturation model, thereby limiting the ability to sustain the force and in turn allowing for consistent increase in cell migration velocity on soft substrate again according to the Hooke’s law and Hill’s muscle equation, respectively. Thus, our model, reproducing the basic trend of the experimental results, provides insights into the mechanisms of environmental cue-dependent migratory behavior of cells.
Assessment of cropland inundation due to the operation of the Reelfoot Lake spillway in West Tennessee
Authors: Bhuyian Md Nowfel M. , Lahiri Chayan , Diehl Timothy H. , Heal Elizabeth N. 
Published: December 2022

AbstractRunning Reelfoot Bayou (RRB) is the outlet canal of Reelfoot Lake, the largest natural lake in Tennessee. RRB is not able to contain discharge from Reelfoot Lake greater than the bankfull discharge of 28 m3/s (1000 ft3/s), which typically occurs at the beginning of the growing season (April–June). Historically, the planting of crops has been delayed until flooding subsides and cropland has drained. The objective of this study is a preliminary quantification of cropland inundation to determine its spatial distribution in the RRB floodplain. Inundated croplands in the RRB floodplain were delineated over a range of spillway discharges from 2 to 57 m3/s (70–2000 ft3/s), using one‐dimensional–two‐dimensional hydrodynamic modeling and multispectral satellite images (Landsat 8 and Sentinel‐2). The composite maps made by combining the simulated and image‐derived flood maps were overlaid on the United States Department of Agriculture CropScape layer to determine the inundation of individual summer crops during the growing season. About 25% of the inundated croplands are flooded at discharges of RRB less than 28 m3/s, implying wetland hydrology. The results of this analysis can be used to inform operational management of the Reelfoot Lake spillway.
Determinants of sexual function in men living with HIV younger than 50 years old: Focus on organic, relational, and psychological issues
Authors: De Vincentis Sara , Decaroli Maria Chiara , Milic Jovana , Fanelli Flaminia , Tartaro Giulia , Diazzi Chiara , Mezzullo Marco , De Santis Maria Cristina , Roli Laura , Trenti Tommaso , Santi Daniele , Pagotto Uberto , Guaraldi Giovanni , Rochira Vincenzo 
Published: December 2022

AbstractBackgroundSexual dysfunctions, particularly erectile dysfunction, are common in men living with HIV, whose organic and psychological components remain to be clarified. The aim of the study is to investigate the impact of risk factors of sexual dysfunctions, including organic, relational, and psychological determinants of erectile function, in men living with HIV younger than 50 years old.MethodsA cross‐sectional, observational study was conducted in men living with HIV < 50 years. The questionnaire International Index of Erectile Function‐15 was used to assess the prevalence and degree of erectile dysfunction. The structured interview of erectile dysfunction was used to explore the organic (Scale 1), relational (Scale 2), and psychological (Scale 3) components of erectile dysfunction. Total testosterone, estradiol, and dihydrotestosterone were measured by liquid chromatography‐tandem‐mass spectrometry; free testosterone was calculated by the Vermeulen equation.ResultsA total of 313 consecutive men living with HIV were prospectively enrolled (median age 47.0 years; median HIV‐infection duration 16.2 years). 187 patients (59.7%) had erectile dysfunction, with a higher prevalence of non‐heterosexual (138 out of 187, 73.8%) than heterosexual patients (p = 0.003). Patients with erectile dysfunction showed a worse score of structured interview of erectile dysfunction scale 3 compared to patients without erectile dysfunction (p = 0.025); the International Index of Erectile Function‐15 was inversely related to structured interview of erectile dysfunction scale 3 (p = 0.042). No difference was found for sex steroids (total testosterone, estradiol, free testosterone, and dihydrotestosterone) between men living with HIV with and without erectile dysfunction. In the multivariate analysis sexual orientation, and lack of stable relationships were major determinants for erectile dysfunction. Only 35 of 187 patients with erectile dysfunction (18.7%) reported the use of erectile dysfunction medications.ConclusionsWithin the multidimensional network of erectile dysfunction in men living with HIV, the psychological component is predominant, highlighting the contribution of peculiar factors related to HIV distress (e.g., fear of virus transmission, stigma) rather than gonadal status and other classical risk factors. In contrast to the high prevalence, only a few patients reported the use of erectile dysfunction medications suggesting a general under‐management of such issues.
Morphine use induces gastric microbial dysbiosis driving gastric inflammation through TLR2 signalling which is attenuated by proton pump inhibition
Authors: Ghosh Nillu , Kesh Kousik , Singh Praveen Kumar , Sharma Umakant , Chupikova Irina , Ramakrishnan Sundaram , Roy Sabita 
Published: December 2022

AbstractBackground and PurposeOpioids are the standard drug for pain management; however, their effects on gastric dysfunction are relatively understudied. Opioid users have a higher incidence of gastric pathology leading to increased hospitalization. Herein, we investigated the consequences of morphine use on gastric pathology and the underlying mechanisms. We further investigated the therapeutic benefit of proton pump inhibition to overcome morphine‐mediated gastric inflammation.Experimental ApproachMice were implanted with 25 mg slow‐release morphine and placebo pellets. Gastric microbiome analyses were performed. Gastric damage was assayed. Gastric pH was measured. Germ‐free and TLR2KO mice were used to investigate the mechanisms. Gastroprotective studies were performed with the proton pump inhibitor (PPI) omeprazole.Key ResultsChronic morphine treatment alters gastric microbial composition and induces preferential expansion of pathogenic bacterial communities such as Streptococcus and Pseudomonas. Morphine causes disruption of the gastric mucosal layer, increases apoptosis, and elevates inflammatory cytokines. Moreover, morphine‐mediated gastric pathology was significantly attenuated in germ‐free mice, and reconstitution of morphine gastric microbiome in germ‐free mice resulted gastric inflammation. In addition, morphine‐mediated gastric inflammation was attenuated in TLR2KO mice. Morphine causes a decrease in gastric pH, which contributes to gastric dysbiosis leads to gastric inflammation. Omeprazole treatment inhibits gastric acidity, rescuing morphine‐induced gastric dysbiosis and preventing inflammation.Conclusion and ImplicationsThis study attributes morphine‐induced gastric acidity as a driver of gastric dysbiosis and pathology and proposes the therapeutic use of PPI as an inexpensive approach for the clinical management of morphine‐associated pathophysiology.