bluuebunny/crossref_metadata_2025_split huggingface dataset:
A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types
Authors: Kozareva Velina , Martin Caroline , Osorno Tomas , Rudolph Stephanie , Guo Chong , Vanderburg Charles , Nadaf Naeem , Regev Aviv , Regehr Wade G. , Macosko Evan 
Published: October 2021

AbstractThe cerebellar cortex is a well-studied brain structure with diverse roles in motor learning, coordination, cognition and autonomic regulation. However, a complete inventory of cerebellar cell types is currently lacking. Here, using recent advances in high-throughput transcriptional profiling1–3, we molecularly define cell types across individual lobules of the adult mouse cerebellum. Purkinje neurons showed considerable regional specialization, with the greatest diversity occurring in the posterior lobules. For several types of cerebellar interneuron, the molecular variation within each type was more continuous, rather than discrete. In particular, for the unipolar brush cells—an interneuron population previously subdivided into discrete populations—the continuous variation in gene expression was associated with a graded continuum of electrophysiological properties. Notably, we found that molecular layer interneurons were composed of two molecularly and functionally distinct types. Both types show a continuum of morphological variation through the thickness of the molecular layer, but electrophysiological recordings revealed marked differences between the two types in spontaneous firing, excitability and electrical coupling. Together, these findings provide a comprehensive cellular atlas of the cerebellar cortex, and outline a methodological and conceptual framework for the integration of molecular, morphological and physiological ontologies for defining brain cell types.
Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH
Authors: Zhang Meng , Eichhorn Stephen W. , Zingg Brian , Yao Zizhen , Cotter Kaelan , Zeng Hongkui , Dong Hongwei , Zhuang Xiaowei 
Published: October 2021

AbstractA mammalian brain is composed of numerous cell types organized in an intricate manner to form functional neural circuits. Single-cell RNA sequencing allows systematic identification of cell types based on their gene expression profiles and has revealed many distinct cell populations in the brain1,2. Single-cell epigenomic profiling3,4 further provides information on gene-regulatory signatures of different cell types. Understanding how different cell types contribute to brain function, however, requires knowledge of their spatial organization and connectivity, which is not preserved in sequencing-based methods that involve cell dissociation. Here we used a single-cell transcriptome-imaging method, multiplexed error-robust fluorescence in situ hybridization (MERFISH)5, to generate a molecularly defined and spatially resolved cell atlas of the mouse primary motor cortex. We profiled approximately 300,000 cells in the mouse primary motor cortex and its adjacent areas, identified 95 neuronal and non-neuronal cell clusters, and revealed a complex spatial map in which not only excitatory but also most inhibitory neuronal clusters adopted laminar organizations. Intratelencephalic neurons formed a largely continuous gradient along the cortical depth axis, in which the gene expression of individual cells correlated with their cortical depths. Furthermore, we integrated MERFISH with retrograde labelling to probe projection targets of neurons of the mouse primary motor cortex and found that their cortical projections formed a complex network in which individual neuronal clusters project to multiple target regions and individual target regions receive inputs from multiple neuronal clusters.
Genetic dissection of the glutamatergic neuron system in cerebral cortex
Authors: Matho Katherine S. , Huilgol Dhananjay , Galbavy William , He Miao , Kim Gukhan , An Xu , Lu Jiangteng , Wu Priscilla , Di Bella Daniela J. , Shetty Ashwin S. , Palaniswamy Ramesh , Hatfield Joshua , Raudales Ricardo , Narasimhan Arun , Gamache Eric , Levine Jesse M. , Tucciarone Jason , Szelenyi Eric , Harris Julie A. , Mitra Partha P. , Osten Pavel , Arlotta Paola , Huang Z. Josh 
Published: October 2021

AbstractDiverse types of glutamatergic pyramidal neurons mediate the myriad processing streams and output channels of the cerebral cortex1,2, yet all derive from neural progenitors of the embryonic dorsal telencephalon3,4. Here we establish genetic strategies and tools for dissecting and fate-mapping subpopulations of pyramidal neurons on the basis of their developmental and molecular programs. We leverage key transcription factors and effector genes to systematically target temporal patterning programs in progenitors and differentiation programs in postmitotic neurons. We generated over a dozen temporally inducible mouse Cre and Flp knock-in driver lines to enable the combinatorial targeting of major progenitor types and projection classes. Combinatorial strategies confer viral access to subsets of pyramidal neurons defined by developmental origin, marker expression, anatomical location and projection targets. These strategies establish an experimental framework for understanding the hierarchical organization and developmental trajectory of subpopulations of pyramidal neurons that assemble cortical processing networks and output channels.
Cellular anatomy of the mouse primary motor cortex
Authors: Muñoz-Castañeda Rodrigo , Zingg Brian , Matho Katherine S. , Chen Xiaoyin , Wang Quanxin , Foster Nicholas N. , Li Anan , Narasimhan Arun , Hirokawa Karla E. , Huo Bingxing , Bannerjee Samik , Korobkova Laura , Park Chris Sin , Park Young-Gyun , Bienkowski Michael S. , Chon Uree , Wheeler Diek W. , Li Xiangning , Wang Yun , Naeemi Maitham , Xie Peng , Liu Lijuan , Kelly Kathleen , An Xu , Attili Sarojini M. , Bowman Ian , Bludova Anastasiia , Cetin Ali , Ding Liya , Drewes Rhonda , D’Orazi Florence , Elowsky Corey , Fischer Stephan , Galbavy William , Gao Lei , Gillis Jesse , Groblewski Peter A. , Gou Lin , Hahn Joel D. , Hatfield Joshua T. , Hintiryan Houri , Huang Junxiang Jason , Kondo Hideki , Kuang Xiuli , Lesnar Philip , Li Xu , Li Yaoyao , Lin Mengkuan , Lo Darrick , Mizrachi Judith , Mok Stephanie , Nicovich Philip R. , Palaniswamy Ramesh , Palmer Jason , Qi Xiaoli , Shen Elise , Sun Yu-Chi , Tao Huizhong W. , Wakemen Wayne , Wang Yimin , Yao Shenqin , Yuan Jing , Zhan Huiqing , Zhu Muye , Ng Lydia , Zhang Li I. , Lim Byung Kook , Hawrylycz Michael , Gong Hui , Gee James C. , Kim Yongsoo , Chung Kwanghun , Yang X. William , Peng Hanchuan , Luo Qingming , Mitra Partha P. , Zador Anthony M. , Zeng Hongkui , Ascoli Giorgio A. , Josh Huang Z. , Osten Pavel , Harris Julie A. , Dong Hong-Wei 
Published: October 2021

AbstractAn essential step toward understanding brain function is to establish a structural framework with cellular resolution on which multi-scale datasets spanning molecules, cells, circuits and systems can be integrated and interpreted1. Here, as part of the collaborative Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based anatomical description of one exemplar brain structure, the mouse primary motor cortex, upper limb area (MOp-ul). Using genetic and viral labelling, barcoded anatomy resolved by sequencing, single-neuron reconstruction, whole-brain imaging and cloud-based neuroinformatics tools, we delineated the MOp-ul in 3D and refined its sublaminar organization. We defined around two dozen projection neuron types in the MOp-ul and derived an input–output wiring diagram, which will facilitate future analyses of motor control circuitry across molecular, cellular and system levels. This work provides a roadmap towards a comprehensive cellular-resolution description of mammalian brain architecture.
Integrating object detection and image segmentation for detecting the tool wear area on stitched image
Authors: Lin Wan-Ju , Chen Jian-Wen , Jhuang Jian-Ping , Tsai Meng-Shiun , Hung Che-Lun , Li Kuan-Ming , Young Hong-Tsu 
Published: October 2021

AbstractFlank wear is the most common wear that happens in the end milling process. However, the process of detecting the flank wear is cumbersome. To achieve comprehensively automatic detecting the flank wear area of the spiral end milling cutter, this study proposed a novel flank wear detection method of combining the template matching and deep learning techniques to expand the curved surface images into panorama images, which is more available to detect the flank wear areas without choosing a specific position of cutting tool image. You Only Look Once v4 model was employed to automatically detect the range of cutting tips. Then, popular segmentation models, namely, U-Net, Segnet and Autoencoder were used to extract the areas of the tool flank wear. To evaluate the segmenting performance among these models, U-Net model obtained the best maximum dice coefficient score with 0.93. Moreover, the predicting wear areas of the U-Net model is presented in the trend figure, which can determine the times of the tool change depend on the curve of the tool wear. Overall, the experiments have shown that the proposed methods can effectively extract the tool wear regions of the spiral cutting tool. With the developed system, users can obtain detailed information about the cutting tool before being worn severely to change the cutting tools in advance.
Rapid transmission of respiratory infections within but not between mountain gorilla groups
Authors: Morrison Robin E. , Mushimiyimana Yvonne , Stoinski Tara S. , Eckardt Winnie 
Published: October 2021

AbstractMinimizing disease transmission between humans and wild apes and controlling outbreaks in ape populations is vital to both ape conservation and human health, but information on the transmission of real infections in wild populations is rare. We analyzed respiratory outbreaks in a subpopulation of wild mountain gorillas (Gorilla beringei beringei) between 2004 and 2020. We investigated transmission within groups during 7 outbreaks using social networks based on contact and proximity, and transmission between groups during 15 outbreaks using inter-group encounters, transfers and home range overlap. Patterns of contact and proximity within groups were highly predictable based on gorillas’ age and sex. Disease transmission within groups was rapid with a median estimated basic reproductive number (R0) of 4.18 (min = 1.74, max = 9.42), and transmission was not predicted by the social network. Between groups, encounters and transfers did not appear to have enabled disease transmission and the overlap of groups’ ranges did not predict concurrent outbreaks. Our findings suggest that gorilla social structure, with many strong connections within groups and weak ties between groups, may enable rapid transmission within a group once an infection is present, but limit the transmission of infections between groups.
A bioinspired neural architecture search based convolutional neural network for breast cancer detection using histopathology images
Authors: Oyelade Olaide N. , Ezugwu Absalom E. 
Published: October 2021

AbstractThe design of neural architecture to address the challenge of detecting abnormalities in histopathology images can leverage the gains made in the field of neural architecture search (NAS). The NAS model consists of a search space, search strategy and evaluation strategy. The approach supports the automation of deep learning (DL) based networks such as convolutional neural networks (CNN). Automating the process of CNN architecture engineering using this approach allows for finding the best performing network for learning classification problems in specific domains and datasets. However, the engineering process of NAS is often limited by the potential solutions in search space and the search strategy. This problem often narrows the possibility of obtaining best performing networks for challenging tasks such as the classification of breast cancer in digital histopathological samples. This study proposes a NAS model with a novel search space initialization algorithm and a new search strategy. We designed a block-based stochastic categorical-to-binary (BSCB) algorithm for generating potential CNN solutions into the search space. Also, we applied and investigated the performance of a new bioinspired optimization algorithm, namely the Ebola optimization search algorithm (EOSA), for the search strategy. The evaluation strategy was achieved through computation of loss function, architectural latency and accuracy. The results obtained using images from the BACH and BreakHis databases showed that our approach obtained best performing architectures with the top-5 of the architectures yielding a significant detection rate. The top-1 CNN architecture demonstrated a state-of-the-art performance of base on classification accuracy. The NAS strategy applied in this study and the resulting candidate architecture provides researchers with the most appropriate or suitable network configuration for using digital histopathology.
Beneficial effects of a mouthwash containing an antiviral phthalocyanine derivative on the length of hospital stay for COVID-19: randomised trial
Authors: da Silva Santos Paulo Sérgio , da Fonseca Orcina Bernardo , Machado Rafael Rahal Guaragna , Vilhena Fabiano Vieira , da Costa Alves Lucas Marques , Zangrando Mariana Schutzer Ragghianti , de Oliveira Rodrigo Cardoso , Soares Mariana Quirino Silveira , Simão Andréa Name Colado , Pietro Emilene Cristine Izu Nakamura , Kuroda Juliana Pescinelli Garcia , de Almeida Benjamim Ivanilda Aparecida , Araujo Danielle Bastos , Toma Sérgio Hiroshi , Flor Lourival , Araki Koiti , Durigon Edison Luiz 
Published: October 2021

AbstractThe risk of contamination and dissemination by SARS-CoV-2 has a strong link with nasal, oral and pharyngeal cavities. Recently, our research group observed the promising performance of an anionic phthalocyanine derivative (APD) used in a mouthwash protocol without photoexcitation; this protocol improved the general clinical condition of patients infected with SARS-CoV-2. The present two-arm study evaluated in vitro the antiviral activity and cytotoxicity of APD. Additionally, a triple-blind randomized controlled trial was conducted with 41 hospitalized patients who tested positive for COVID-19. All the included patients received World Health Organization standard care hospital treatment (non-intensive care) plus active mouthwash (experimental group AM/n = 20) or nonactive mouthwash (control group NAM/n = 21). The adjunct mouthwash intervention protocol used in both groups consisted one-minute gargling/rinsing / 5 times/day until hospital discharge. Groups were compared considering age, number of comorbidities, duration of symptoms prior admission and length of hospital stay (LOS). The associations between group and sex, age range, presence of comorbidities, admission to Intensive care unit (ICU) and death were also evaluated. The in vitro evaluation demonstrated that APD compound was highly effective for reduction of SARS-CoV-2 viral load in the 1.0 mg/mL (99.96%) to 0.125 mg/mL (92.65%) range without causing cytotoxicity. Regarding the clinical trial, the median LOS of the AM group was significantly shortened (4 days) compared with that of the NAM group (7 days) (p = 0.0314). Additionally, gargling/rinsing with APD was very helpful in reducing the severity of symptoms (no ICU care was needed) compared to not gargling/rinsing with APD (28.6% of the patients in the NAM group needed ICU care, and 50% of this ICU subgroup passed way, p = 0.0207). This study indicated that the mechanical action of the protocol involving mouthwash containing a compound with antiviral effects against SARS-CoV-2 may reduce the symptoms of the patients and the spread of infection. The use of APD in a mouthwash as an adjuvant the hospital COVID-19 treatment presented no contraindication and reduced the hospital stay period.Trial registration: The clinical study was registered at REBEC—Brazilian Clinical Trial Register (RBR-58ftdj).
The Drake Passage opening from an experimental fluid dynamics point of view
Authors: Vincze Miklós , Bozóki Tamás , Herein Mátyás , Borcia Ion Dan , Harlander Uwe , Horicsányi Attila , Nyerges Anita , Rodda Costanza , Pál András , Pálfy József 
Published: October 2021

AbstractPronounced global cooling around the Eocene–Oligocene transition (EOT) was a pivotal event in Earth’s climate history, controversially associated with the opening of the Drake Passage. Using a physical laboratory model we revisit the fluid dynamics of this marked reorganization of ocean circulation. Here we show, seemingly contradicting paleoclimate records, that in our experiments opening the pathway yields higher values of mean water surface temperature than the “closed” configuration. This mismatch points to the importance of the role ice albedo feedback plays in the investigated EOT-like transition, a component that is not captured in the laboratory model. Our conclusion is supported by numerical simulations performed in a global climate model (GCM) of intermediate complexity, where both “closed” and “open” configurations were explored, with and without active sea ice dynamics. The GCM results indicate that sea surface temperatures would change in the opposite direction following an opening event in the two sea ice dynamics settings, and the results are therefore consistent both with the laboratory experiment (slight warming after opening) and the paleoclimatic data (pronounced cooling after opening). It follows that in the hypothetical case of an initially ice-free Antarctica the continent could have become even warmer after the opening, a scenario not indicated by paleotemperature reconstructions.
AHA1 regulates cell migration and invasion via the EMT pathway in colorectal adenocarcinomas
Authors: Kim Dasom , Moon Ji Wook , Min Dong Hwa , Ko Eun Sun , Ahn Bokyung , Kim Eun Sun , Lee Ji-Yun 
Published: October 2021

AbstractThe progression of colorectal cancer (CRC) has been well studied and understood with the development of molecular and genetic techniques. However, specific marker(s) that could be used to predict lymph node (LN) involvement, which is the most important prognostic factor for CRC, have not been identified so far. Our previous study, in which network analysis of LN(+) and LN(−) CRC gene expression was carried out with data obtained from the Cancer Genome Atlas, led to the identification ofAHA1.AHA1is a co-chaperone activator of the Hsp90 ATPase activity. However, the role ofAHA1expression in cancer cells is still unclear. To investigate howAHA1expression regulates the cancer cell progression and/or metastasis of human CRC, the expression levels ofAHA1and Hsp90 were examined in 105 CRC tissue samples and compared with those in paired normal tissue. The RNA expression levels ofAHA1and Hsp90aa1, but not Hsp90ab, were significantly higher in cancer tissues than in adjacent paired normal tissues (p = 0.032 and p = 0.0002, respectively). In particular,AHA1, but not Hsp90aa1 and Hsp90ab, was closely associated with the TNM stage, LN stage, and tumor metastasis (p = 0.035, p = 0.012, and p = 0.0003, respectively). Moreover, the expression ofAHA1was not only higher in the CRC cell lines than in the normal colon fibroblast cell line but was also associated with the progression of these CRC cell lines. Overexpression ofAHA1in SW480 cells increased, whereas suppression ofAHA1expression in HCT116 cells reduced cell migration and invasion through the regulation of Snail, E-cadherin, pSRC, and pAKT, which are associated with EMT signaling. Taken together, our study suggests thatAHA1contributes to the metastatic advantage of human CRC.
Atomistic mechanisms for frictional energy dissipation during continuous sliding
Authors: Krylov S. Yu. , Frenken J. W. M. 
Published: October 2021

AbstractAfter more than a century of detailed investigations into sliding friction, we have not arrived yet at a basic understanding of energy dissipation, even for the simple geometry of a rigid slider moving over a perfectly periodic counter surface. In this article, we use a first-principles-based analysis to establish the atomistic mechanisms of frictional energy dissipation for a rigid object that moves continuously in the periodic surface potential landscape of a solid with vibrational degrees of freedom. We identify two mechanisms that can be viewed as (i) the continuous pumping of energy into the resonant modes, if these exist, and (ii) the destructive interference of the force contributions introduced by all excited phonon modes. These mechanisms act already in a purely dynamic system that includes independent, non-interacting phonon modes, and they manifest irreversibility as a kind of “dynamical stochastization”. In contrast to wide-spread views, we show that the transformation of mechanical energy into heat, that always takes place in real systems due to the coupling between phonon modes, can play only a minor role in the appearance of friction, if any. This insight into the microscopic mechanisms of energy dissipation opens a new, direct way towards true control over friction.
Incidence, causes and consequences of moderate and severe traumatic brain injury as determined by Abbreviated Injury Score in the Netherlands
Authors: Jochems Denise , van Rein Eveline , Niemeijer Menco , van Heijl Mark , van Es Michael A. , Nijboer Tanja , Leenen Luke P. H. , Houwert R. Marijn , van Wessem Karlijn J. P. 
Published: October 2021

AbstractTraumatic brain injury (TBI) is a leading cause of death and disability. Epidemiology seems to be changing. TBIs are increasingly caused by falls amongst elderly, whilst we see less polytrauma due to road traffic accidents (RTA). Data on epidemiology is essential to target prevention strategies. A nationwide retrospective cohort study was conducted. The Dutch National Trauma Database was used to identify all patients over 17 years old who were admitted to a hospital with moderate and severe TBI (AIS ≥ 3) in the Netherlands from January 2015 until December 2017. Subgroup analyses were done for the elderly and polytrauma patients. 12,295 patients were included in this study. The incidence of moderate and severe TBI was 30/100.000 person-years, 13% of whom died. Median age was 65 years and falls were the most common trauma mechanism, followed by RTAs. Amongst elderly, RTAs consisted mostly of bicycle accidents. Mortality rates were higher for elderly (18%) and polytrauma patients (24%). In this national database more elderly patients who most often sustained the injury due to a fall or an RTA were seen. Bicycle accidents were very frequent, suggesting prevention could be an important aspect in order to decrease morbidity and mortality.