bluuebunny/crossref_metadata_2025_split huggingface dataset:
The challenges of diabetic polyneuropathy: a brief update
Authors: Zochodne Douglas W. 
Published: July 2019

Purpose of review
The current review addresses one of the most common neurological disorders, diabetic polyneuropathy (DPN). DPN is debilitating, irreversible and dwarfs the prevalence of most other chronic disorders of the nervous system. Its complications include foot ulceration, amputation, falling and intractable neuropathic pain. Moreover, tight control of hyperglycemia reduces the incidence of DPN in type 1 diabetes mellitus but its role in type 2 diabetes mellitus is less clear.

Recent findings
New therapeutic options to reverse the development of DPN or its associated pain have been proposed but none have significantly changed the clinical approach. The cause of DPN remains controversial traditionally focused on the impact of metabolic abnormalities, polyol flux, microvascular changes, mitochondria, oxidative stress, lipid biology and others. In particular, there has been less attention toward how this chronic disorder alters peripheral neurobiology. It is now clear that in chronic models of diabetes mellitus there exists a unique form of neurodegeneration with a range of protein, mRNA and microRNA alterations to consider. How to reconcile these molecular and structural alterations with metabolic mechanisms is a challenge. In sensory neurons alone, a primary target of DPN, both central perikaryal cytoplasmic and nuclear changes and altered distal sensory axon terminal plasticity may be involved.

Summary
In this review, the current therapeutic status of DPN is described with greater emphasis on some new but selected thoughts on its neurobiology. New mechanistic understanding will be essential to developing precision therapeutics for DPN.
Update on classification, epidemiology, clinical phenotype and imaging of the nonsystemic vasculitic neuropathies
Authors: Collins Michael P. , Dyck P. James B. , Hadden Robert D.M. 
Published: July 2019

Purpose of review
Single-organ vasculitis of the peripheral nervous system (PNS) is often designated nonsystemic vasculitic neuropathy (NSVN). Several variants or subtypes have been distinguished, including migratory sensory neuropathy, postsurgical inflammatory neuropathy, diabetic radiculoplexus neuropathies, skin-nerve vasculitides, and, arguably, neuralgic amyotrophy. NSVN often presents as nondiabetic lumbosacral radiculoplexus neuropathy (LRPN). This review updates classification, clinical features, epidemiology, and imaging of these disorders.

Recent findings
A recent study showed the annual incidence of LRPN in Olmstead County, Minnesota to be 4.16/100 000:2.79/100 000 diabetic and 1.27/100 000 nondiabetic. This study was the first to determine the incidence or prevalence of any vasculitic neuropathy. In NSVN, ultrasonography shows multifocal enlargement of proximal and distal nerves. In neuralgic amyotrophy, MRI and ultrasound reveal multifocal enlargements and focal constrictions in nerves derived from the brachial plexus. Histopathology of these chronic lesions shows inflammation and rare vasculitis. Diffusion tensor imaging of tibial nerves in NSVN revealed decreased fractional anisotropy in one study.

Summary
Single-organ PNS vasculitides are the most common inflammatory neuropathies. Neuralgic amyotrophy might result from PNS vasculitis, but further study is necessary. The usefulness of focal nerve enlargements or constrictions in understanding pathological mechanisms, directing biopsies, and monitoring disease activity in NSVN should be further investigated.
Prediagnostic breast milk DNA methylation alterations in women who develop breast cancer
Authors: Salas Lucas A , Lundgren Sara N. , Browne Eva P. , Punska Elizabeth C. , Anderton Douglas L. , Karagas Margaret R , Arcaro Kathleen F. , Christensen Brock C. 
Published: July 2019

ABSTRACTBackgroundPrior candidate gene studies have shown tumor suppressor DNA methylation in breast milk related with history of breast biopsy, an established risk factor for breast cancer. To further establish the utility of breast milk as a tissue-specific biospecimen for investigations of breast carcinogenesis we measured genome-wide DNA methylation in breast milk from women with and without a diagnosis of breast cancer in two independent cohorts.MethodsDNA methylation was assessed using Illumina HumanMethylation450k in 87 breast milk samples. After quality control, 368,171 autosomal CpG loci were analyzed. Cell type proportion estimates from RefFreeCellMix were calculated and adjusted for in this Epigenome Wide Association Study using linear mixed effects models adjusted for history of breast biopsy, age, time of delivery, cell type proportion estimates, array chip, and subject as random effect.ResultsEpigenome-wide analyses identified 58 differentially methylated CpG sites associated with a breast cancer diagnosis in the prospectively collected milk samples from the breast that would develop cancer compared with women without a diagnosis of breast cancer (q-value < 0.05). Nearly all CpG sites associated with a breast cancer diagnosis were hypomethylated in cases compared with controls, and were enriched for CpG islands. In addition, inferred repeat element methylation was lower in breast milk DNA from cases compared to controls, and cases exhibited increased estimated epigenetic mitotic tick rate as well as DNA methylation age compared with controls.ConclusionBreast milk has utility as a biospecimen for prospective assessment of disease risk, for understanding the underlying molecular basis of breast cancer risk factors, and improving primary and secondary prevention of breast cancer.
Increased functional connectivity of thalamic subdivisions in patients with Parkinson’s disease
Authors: Owens-Walton Conor , Jakabek David , Power Brian D. , Walterfang Mark , Velakoulis Dennis , van Westen Danielle , Looi Jeffrey C.L. , Shaw Marnie , Hansson Oskar 
Published: July 2019

AbstractParkinson’s disease (PD) affects 2-3% of the population over the age of 65 with loss of dopaminergic neurons in the substantia nigra impacting the functioning of basal ganglia-thalamocortical circuits. The precise role played by the thalamus is unknown, despite its critical role in the functioning of the cerebral cortex, and the abnormal neuronal activity of the structure in PD. Our objective was to more clearly elucidate how functional connectivity and morphology of the thalamus are impacted in PD (n= 32) compared to Controls (n= 20). To investigate functional connectivity of the thalamus we subdivided the structure into two important regions-of-interest, the first with putative connections to the motor cortices and the second with putative connections to prefrontal cortices. We then investigated potential differences in the size and shape of the thalamus in PD, and how morphology and functional connectivity relate to clinical variables. Our data demonstrate that PD is associated with increases in functional connectivity between motor subdivisions of the thalamus and the supplementary motor area, and between prefrontal thalamic subdivisions and nuclei of the basal ganglia, anterior and dorsolateral prefrontal cortices, as well as the anterior and paracingulate gyri. These results suggest that PD is associated with increased functional connectivity of subdivisions of the thalamus which may be indicative alterations to basal ganglia-thalamocortical circuitry.
Enhancing single-cell cellular state inference by incorporating molecular network features
Authors: Dong Ji , Zhou Peijie , Wu Yichong , Wang Wendong , Chen Yidong , Zhou Xin , Xie Haoling , Gao Yuan , Lu Jiansen , Yang Jingwei , Zhang Xiannian , Wen Lu , Fu Wei , Li Tiejun , Tang Fuchou 
Published: July 2019

AbstractIn biological systems, genes function in conjunction rather than in isolation. However, traditional single-cell RNA-seq (scRNA-seq) analyses heavily rely on the transcriptional similarity of individual genes, ignoring the inherent gene-gene interactions. Here, we present SCORE, a network-based method, which incorporates the validated molecular network features to infer cellular states. Using real scRNA-seq datasets, SCORE outperforms existing methods in accuracy, robustness, scalability, data integration and removal of batch effect. When applying SCORE to a newly generated human ileal scRNA-seq dataset, we identified several novel stem/progenitor clusters, including a Cripto-1+ cluster. Moreover, two distinct groups of goblet cells were identified and only one of them tended to secrete mucus. Besides, we found that the recently identified BEST4+OTOP2+ microfold cells also highly expressed CFTR, which is different from their colonic counterparts. In summary, SCORE enhances cellular state inference by simulating the dynamic changes of molecular networks, providing more biological insights beyond statistical interpretations.
Liver fluke granulin promotes exosome-mediated crosstalk and cellular microenvironment conducive to cholangiocarcinoma
Authors: Arunsan Patpicha , Chaidee Apisit , Cochan Christina J. , Mann Victoria H. , Tanno Toshihiko , Kumkhaek Chutima , Smout Michael J. , Karinshak Shannon E. , Rodpai Rutchanee , Sotillo Javier , Loukas Alex , Laha Thewarach , Brindley Paul J. , Ittiprasert Wannaporn 
Published: July 2019

AbstractCrosstalk between malignant and neighboring cells contributes to tumor growth. In East Asia, infection with fish-borne liver flukes is a major risk factor for cholangiocarcinoma (CCA). The parasite secretes a growth factor termed liver fluke granulin (Ov-GRN-1), a homologue of the human progranulin (huPGRN), which contributes significantly to biliary tract fibrosis and morbidity during infection. Here, exosome-mediated transfer of mRNAs from the human cholangiocyte cell line (H69) was investigated following exposure to Ov-GRN-1, to naïve recipient H69 cells. To minimize the influence of endogenous huPGRN, the gene encoding huPGRN was inactivated using CRISPR/Cas9-based gene knock-out. Several huPGRN-depleted cell lines, termed ΔhuPGRN-H69, were established. These lines exhibited >80% reductions in levels of huPGRN transcripts and protein, both in gene-edited cells and within exosomes released by these cells. Profiles of exosomal RNAs (exRNA) from ΔhuPGRN-H69 for CCA-associated characteristics revealed a paucity of transcripts for estrogen- and Wnt-signaling pathways, peptidase inhibitors and tyrosine phosphatase related to cellular processes including oncogenic transformation. Several CCA-specific mRNAs including MAPK/AKT pathway members were induced by exposure to Ov-GRN-1. By comparison, estrogen, Wnt/PI3K and TGF signaling and other CCA pathway mRNAs were upregulated in wild type H69 exposed to Ov-GRN-1. Of these, CCA-associated exRNAs modified the CCA microenvironment in naïve recipient cells co-cultured with exosomes from ΔhuPGRN-H69 exposed to Ov-GRN-1, and induced translation of MAPK phosphorylation related-protein in naïve recipient cells comparing with control recipient cells. Exosome-mediated crosstalk in response to liver fluke granulin promoted a CCA-specific program through MAPK pathway which, in turn, established a CCA-conducive disposition.
Functional connectivity predicts changes in attention over minutes, days, and months
Authors: Rosenberg Monica D. , Scheinost Dustin , Greene Abigail S. , Avery Emily W. , Kwon Young Hye , Finn Emily S. , Ramani Ramachandran , Qiu Maolin , Constable R. Todd , Chun Marvin M. 
Published: July 2019

AbstractThe ability to sustain attention differs across people and changes within a single person over time. Although recent work has demonstrated that patterns of functional brain connectivity predict individual differences in sustained attention, whether these same patterns capture fluctuations in attention in single individuals remains unclear. Here, across five independent studies, we demonstrate that the sustained attention connectome-based predictive model (CPM), a validated model of sustained attention function, generalizes to predict attention changes across minutes, days, weeks, and months. Furthermore, the sustained attention CPM is sensitive to within-subject state changes induced by propofol as well as sevoflurane, such that individuals show functional connectivity signatures of stronger attentional states when awake than when under deep sedation and light anesthesia. Together these results demonstrate that fluctuations in attentional state reflect variability in the same functional connectivity patterns that predict individual differences in sustained attention.
Alternative splicing modulation by G-quadruplexes
Authors: Georgakopoulos-Soares Ilias , Parada Guillermo E. , Wong Hei Yuen , Miska Eric A. , Kwok Chun Kit , Hemberg Martin 
Published: July 2019

AbstractAlternative splicing is central to metazoan gene regulation but the regulatory mechanisms involved are only partially understood. Here, we show that G-quadruplex (G4) motifs are enriched ~3-fold both upstream and downstream of splice junctions. Analysis of in vitro G4-seq data corroborates their formation potential. G4s display the highest enrichment at weaker splice sites, which are frequently involved in alternative splicing events. The importance of G4s in RNA as supposed to DNA is emphasized by a higher enrichment for the non-template strand. To explore if G4s are involved in dynamic alternative splicing responses, we analyzed RNA-seq data from mouse and human neuronal cells treated with potassium chloride. We find that G4s are enriched at exons which were skipped following potassium ion treatment. We validate the formation of stable G4s for three candidate splice sites by circular dichroism spectroscopy, UV-melting and fluorescence measurements. Finally, we explore G4 motifs across eleven representative species, and we observe that strong enrichment at splice sites is restricted to mammals and birds.
Self-assembled primary tumor clusters for precision cancer therapy
Authors: Yin Shenyi , Xi Ruibin , Wu Aiwen , Ji Jia-Fu , Xi Jianzhong Jeff 
Published: July 2019

AbstractSeveral patient-derived tumor models emerged recently as robust preclinical models. However, their potential to guide clinical therapy remained unclear. We report a novel model for personalized drug testing called patient-derived tumor-like cell clusters (PTC) that enabled us to accomplish personalized drug tests within 10-20 days. Mechanistically, PTCs result from the migration and aggregation of CD8+/CD44+ primary epithelial cells in a mixture of fibroblasts and macrophages, and form spheroid cultures. Phenotypic and genotypic profiling of PTCs showed a high degree of similarity with the original patient tumors, indicating that PTC structurally and functionally recapitulated original tumors. Over 200 PTC models have been established from at least six cancer types and diverse sampling approaches. Given its seamless integration with current clinical sampling approaches, the PTC platform will revolutionize chemotherapy programs for cancer patients.
Pivotal involvement of the CX3CL1-CX3CR1 axis for the recruitment of M2-TAMs in skin carcinogenesis
Authors: Ishida Yuko , Kuninaka Yumi , Yamamoto Yuki , Nosaka Mizuho , Kimura Akihiko , Furukawa Fukumi , Mukaida Naofumi , Kondo Toshikazu 
Published: July 2019

ABSTRACTWe previously revealed the crucial roles of CX3CL1-CX3CR1 axis in skin wound healing. Although repeated wounds frequently develop into skin cancer, the roles of CX3CL1 in skin carcinogenesis remain elusive. Here, we proved that CX3CL1 protein expression and CX3CR1+ macrophages were observed in human skin cancer tissues. Similarly, we observed the enhancement of CX3CL1 expression and the abundant accumulation of CX3CR1+ tumor-associated macrophages (TAMs) with M2 phenotypes in the skin carcinogenesis process induced by the combined treatment with 7,12-dimethylbenz-(a)anthracene (DMBA) and 12-O-tetradecanoylphorbol-13-acetate (TPA). In this mouse skin carcinogenesis process, CX3CR1+ TAMs exhibited M2 phenotypes with the expression of Wnt3a and angiogenic molecules including vascular endothelial growth factor (VEGF) and matrix metalloproteinase (MMP)-9. Compared to wild-type mice, CX3CR1-deficient mice showed fewer numbers of skin tumors with a lower incidence. Concomitantly, M2-macrophage numbers and neovascularization reduced with the depressed expression of angiogenic factors and Wnt3a. Thus, the CX3CL1-CX3CR1 axis can crucially contribute to skin carcinogenesis by regulating the accumulation and functions of TAMs. Thus, this axis can be a good target for preventing and/or treating skin cancers.
DIscBIO: a user-friendly pipeline for biomarker discovery in single-cell transcriptomics
Authors: Ghannoum Salim , Netto Waldir Leoncio , Fantini Damiano , Ragan-Kelley Benjamin , Parizadeh Amirabbas , Jonasson Emma , Ståhlberg Anders , Farhan Hesso , Köhn-Luque Alvaro 
Published: July 2019

AbstractThe growing attention toward the benefits of single-cell RNA sequencing (scRNA-seq) is leading to a myriad of computational packages for the analysis of different aspects of scRNA-seq data. For researchers without advanced programing skills, it is very challenging to combine several packages in order to perform the desired analysis in a simple and reproducible way. Here we present DIscBIO, an open-source, multi-algorithmic pipeline for easy, efficient and reproducible analysis of cellular sub-populations at the trasncriptomic level. The pipeline integrates multiple scRNA-seq packages and allows biomarker discovery with decision trees and gene enrichment analysis in network context using single-cell sequencing read counts through clustering and differential analysis. DIscBIO is freely available as an R package. It can be run either in command-line mode or through a computational pipeline using Jupyter notebooks. We also provide a user-friendly, cloud version of the notebook for researchers with very limited programming skills. We showcase all pipeline features using two scRNA-seq datasets. The first dataset consists of circulating tumor cells from patients with breast cancer. The second one is a cell cycle regulation datatset in myxoid liposarcoma. All analyses are available as notebooks that integrate in a sequential narrative R code with explanatory text and output data and images. These notebooks can be used as tutorials for training purposes and will guide researchers to explore their scRNA-seq data.
Isothermal digital detection of microRNA using background-free molecular circuit
Authors: Gines Guillaume , Menezes Roberta , Nara Kaori , Kirstetter Anne-Sophie , Taly Valérie , Rondelez Yannick 
Published: July 2019

AbstractMicroRNA, a class of transcripts involved in the regulation of gene expression, are emerging as promising disease-specific biomarkers accessible from tissues or bodily fluids. However, their accurate quantification from biological samples remains challenging. We report a sensitive and quantitative microRNA method using an isothermal amplification chemistry adapted to a droplet digital readout. Building on molecular programming concepts, we design DNA circuit that converts, threshold, amplifies and report the presence of a specific microRNA, down to the femtomolar concentration. Using a leak-absorption mechanism, we were able to suppress non-specific amplification, classically encountered in other exponential amplification reactions. As a result, we demonstrate that this isothermal amplification scheme is adapted to digital counting of microRNA: by partitioning the reaction mixture into water-in-oil droplets, resulting in single microRNA encapsulation and amplification, the method provides absolute target quantification. The modularity of our approach enables to repurpose the assay for various microRNA sequences.
Variation in cephalic neuromasts surface and cave-dwelling fishes of the family Amblyopsidae (Teleostei: Percopsiformes)
Authors: Soares Daphne , Niemiller Matthew L. 
Published: July 2019

AbstractCave adaptation has led to unique sensory specializations to compensate for the lack of visual cues in aphotic subterranean habitats. As the role of vision is reduced or disappears, other sensory modalities become hypertrophied allowing cave-adapted organisms to successfully detect and interact their surrounding environment. The array of aquatic subterranean habitats, from fast-flowing streams and waterfalls, to quiet phreatic pools, presents a diverse palette to examine what possible sensory solutions have evolved against a backdrop of complete darkness. Mechanosensation is enhanced in many subterranean animals to such an extent that a longer appendage is recognized as a prominent troglomorphic adaptation in many metazoans. Fishes, however, not only interact with the environment using their fins, but also with specialized sensory organs to detect hydrodynamic events. We hypothesize that subterranean adaptation drives the hypertrophy of the mechanosensory lateral line, but that other environmental forces dictate the specific neuromast phenotype. To this end, we studied differences in the cephalic lateral line of the fishes in the North American family Amblyopsidae, which includes surface, cave-facultative, and cave-obligate species. None of the taxa we examined possessed canal neuromasts on the head. Primarily surface-dwelling species,Chologaster cornutaandForbesichthys agassizii, possessed receded neuromasts throughout most of the head, with a few on papillae located in front of the nostrils and on ventral grooves on each side of the mouth. The cavefishesAmyblopsis spelaeaandTyphlichthys subterraneouspossessed papillate superficial neuromasts all over the head. We speculate that the change from the surface to the cave environment has led to papillate neuromasts in this group, which are likely shaped to detect the hydrodynamic characteristics of the boundary layer created by the swimming fish. Moving sensory organs from the surface of the body out into the boundary layer could increase sensitivity to high frequency stimuli created by prey, predators, and conspecifics.
LSM2-8 and XRN-2 contribute to the silencing of H3K27me3-marked genes through targeted RNA decay
Authors: Mattout Anna , Gaidatzis Dimos , Padeken Jan , Schmid Christoph , Aeschlimann Florian , Kalck Véronique , Gasser Susan M. 
Published: July 2019

SummaryIn fission yeast and plants, RNA-processing pathways contribute to constitutive and facultative heterochromatin silencing, complementing well-characterized pathways of transcriptional repression. However, it was unclear whether this additional level of regulation occurs in metazoans. Here we describe a pathway of silencing in C. elegans somatic cells, in which the highly conserved, RNA binding complex LSM2-8 selectively silences heterochromatic reporters and endogenous genes bearing the Polycomb mark H3K27me3. Importantly, the LSM2-8 complex works cooperatively with XRN-2, a 5’-3’ exoribonuclease, and disruption of the pathway leads to mRNA stabilization. This selective LSM2-8-mediated RNA degradation does not target nor depend on H3K9me2/me3, unlike previously described pathways of heterochromatic RNA degradation. Intriguingly, the loss of LSM2-8 coincides with a localized drop in H3K27me3 levels on lsm-8-sensitive loci only. Together this defines a mechanism of RNA degradation that selectively targets a subset of H3K27me3-marked genes, revealing an unrecognized layer of regulation for facultative heterochromatin in animals.