bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kappa (κ): Analysis of Curvature in Biological Image Data using B-splines
Authors: Mary Hadrien , Brouhard Gary J. 
Published: November 2019

AbstractCurvature is a central morphological feature of tissues, cells, and sub-cellular structures. A challenge for computational biology is to measure the curvature of these structures from biological image data. We present an open-source Fiji plugin for measuring curvature using B-splines. The plugin is named Kappa after the Greek symbol for curvature, κ. Kappa is semi-automated: users create an initialization curve by a point-click method, and the initialization curve is fit to the underlying data using an iterative minimization algorithm. We demonstrate Kappa’s applicability on images of cytoskeletal filaments in vitro, the cell wall of budding yeast, and whole worms moving in an agar dish. In order to verify the accuracy and precision of Kappa, we created a bank of synthetic images of known curvature using sine waves and golden spirals, which we digitized with different signal-to-noise ratios (SNR), pixel sizes, and point-spread functions (PSF). For synthetic images with characteristics similar to real data, the measured curvatures of those images show a high correlation with the theoretical curvatures. Our fitting algorithms perform better with higher SNR, smaller pixel sizes, and especially PSFs equivalent to super-resolution microscopy data (surprise, surprise). Kappa is freely available under the MIT license for simple integration into Fiji-based workflows. The source code and documentation can be found on GitHub at https://github.com/brouhardlab/Kappa.
Learning to Fold RNAs in Linear Time
Authors: Rezaur Rahman Chowdhury F A , Zhang He , Huang Liang 
Published: November 2019

AbstractRNA secondary structure is helpful for understanding RNA’s functionality, thus accurate prediction systems are desired. Both thermodynamics-based models and machine learning-based models have been used in different prediction systems to solve this problem. Compared to thermodynamics-based models, machine learning-based models can address the inaccurate measurement of thermodynamic parameters due to experimental limitation. However, the existing methods for training machine learning-based models are still expensive because of their cubic-time inference cost. To overcome this, we present a linear-time machine learning-based folding system, using recently proposed approximate folding tool LinearFold as inference engine, and structured SVM (sSVM) as training algorithm. Furthermore, to remedy non-convergence of naive sSVM with inexact search inference, we introduce a max violation update strategy. The training speed of our system is 41× faster than CONTRAfold on a diverse dataset for one epoch, and 14× faster than MXfold on a dataset with longer sequences. With the learned parameters, our system improves the accuracy of LinearFold, and is also the most accurate system among selected folding tools, including CONTRAfold, Vienna RNAfold and MXfold.
A human-specific modifier of cortical circuit connectivity and function improves behavioral performance
Authors: Schmidt Ewoud R.E. , Zhao Hanzhi T. , Park Jung M. , Dahan Jacob B. , Rodgers Chris C. , Hillman Elizabeth M. C. , Bruno Randy M. , Polleux Franck 
Published: November 2019

SUMMARYThe remarkable cognitive abilities characterizing humans are thought to emerge from our unique features of cortical circuit architecture, including increased feedforward and feedback connectivity. However, our understanding of the evolutionary origin and nature of these changes in circuit connectivity, and how they impact cortical circuit function and behavior is currently lacking. Here, we demonstrate that expression of the human-specific gene duplication SRGAP2C leads to a specific increase in feedforward and feedback cortico-cortical connectivity. Moreover, humanized SRGAP2C mice display improved cortical sensory coding, and an enhanced ability to learn a cortex-dependent sensory discrimination task. Our results identify a novel substrate for human brain evolution whereby the emergence of SRGAP2C led to increased feedforward and feedback cortico-cortical connectivity, improved cortical sensory processing and enhanced behavioral performance.
Rapid antimicrobial susceptibility test using spatiotemporal analysis of laser speckle dynamics of bacterial colonies
Authors: Han SeungYun , No Hojun , Baek YoonSeok , Park Huijun , Lee KyeoReh , Yang Seungbum , Park YongKeun 
Published: November 2019

ABSTRACTAntimicrobial susceptibility testing (AST) is crucial for providing appropriate choices and doses of antibiotics to patients. However, standard ASTs require a time-consuming incubation of about 16-20 h for visual accumulation of bacteria, limiting the use of AST for an early prescription. In this study, we propose a rapid AST based on laser speckle formation (LSF) that enables rapid detection of bacterial growth, with the same sample preparation protocol as in solid-based ASTs. The proposed method exploits the phenomenon that well-grown bacterial colonies serve as optical diffusers, which convert a plane-wave laser beam into speckles. The generation of speckle patterns indicates bacterial growth at given antibiotic concentrations. Speckle formation is evaluated by calculating the spatial autocorrelation of speckle images, and bacterial growth is determined by tracking the autocorrelation value over time. We demonstrated the performance of the proposed method for several combinations of bacterial species and antibiotics to achieve the AST in 2-4.5 hours. Furthermore, we also demonstrated the sensitivity of the technique for low bacterial density. The proposed method can be a powerful tool for rapid, simple, and low-cost AST.Abstract Figure
A simple computer vision algorithm as a clinical aid for the pathologist
Authors: Lázaro-Guevara J.M. , Flores-Robles B.J. , Murga A.E. , Garrido K.M. 
Published: November 2019

AbstractHistological analysis for cancer detection or stratification is performed by observing and examining a small portion of a biopsied tissue under a microscope. Nevertheless, to assign clinical meaning to the findings, the analysis and interpretation of an experienced Pathologist is always necessary. Using high-resolution images, these experts visually examine the sample looking for specific characteristics on the cell shapes and tissue distributions, so they could decide whether tissue regions are cancerous, and establish the malignancy level of it. However, with the increasing demand for work for those pathologists and the importance of accuracy on diagnostics, multiple attempts to simplify their work have been performed. Current Imaging technologies allow novel horizons in the automatized selection of some of the characteristics that indicate malignancy in a biopsy. In this work, we propose a simple computer vision algorithm that can be implemented as a screening method for focusing in histological areas with higher risk of malignancy saving time to the pathologist and helping to perform a more standardized work, an easy observation with the potential to become in an aid to daily clinical work.
Push-to-open: The Gating Mechanism of the Tethered Mechanosensitive Ion Channel NompC
Authors: Wang Yang , Guo Yifeng , Liu Chunhong , Wang Lei , Zhang Aihua , Yan Zhiqiang , Song Chen 
Published: November 2019

AbstractNompC was one of the earliest identified mechanosensitive ion channels responsible for the sensation of touch and balance in Drosophila melanogaster. A tethered gating model was proposed for NompC and the Cryo-EM structure has been solved. However, the atomistic mechano-gating mechanism still remains elusive. Here we show the atomistic details of the NompC channel opening in response to the compression of the intracellular domain while remaining closed under an intracellular stretch. This is demonstrated by all-atom molecular dynamics simulations and evidenced by electrophysiological experiments. Under intracellular compression, the ankyrin repeat region undergoes a significant conformational change and passes the mechanical force to the linker helices like a spring with a force constant of ~3.3 pN/nm. The linker helix region acts as a bridge between the ankyrin repeats and TRP domain, and most of the mutations breaking the hydrogen bonds around this region lead to the loss-of-function of the channel. Eventually, the compression-induced mechanical force is passed from the linker helices onto the TRP domain, which then undergoes a clockwise rotation that leads to the opening of the channel. This work provides a clear picture of how a pushing force opens the mechanosensitive ion channel NompC, which might be a universal gating mechanism of similar tethered mechanosensitive ion channels, enabling cells to feel and respond to compression or shrinking.
Ectopic HCN4 expression drives mTOR-dependent epilepsy
Authors: Hsieh Lawrence S. , Wen John H. , Nguyen Lena H. , Zhang Longbo , Torres-Reveron Juan , Spencer Dennis D. , Bordey Angélique 
Published: November 2019

AbstractThe causative link between focal cortical malformations (FCM) and epilepsy is well-accepted, especially among patients with focal cortical dysplasia type II (FCDII) and tuberous sclerosis complex (TSC). However, the mechanisms underlying seizures remain unclear. Using a mouse model of TSC- and FCDII-associated FCM, we show that FCM neurons are responsible for seizure activity via their unexpected abnormal expression of the hyperpolarization-activated cyclic nucleotide-gated potassium channel isoform 4 (HCN4), which is normally not present in cortical pyramidal neurons after birth. Increasing intracellular cAMP levels, which preferentially affects HCN4 gating relative to the other isoforms, drove repetitive firing of FCM neurons but not that of control pyramidal neurons. Ectopic HCN4 expression was mTOR-dependent, preceded the onset of seizures, and was also found in diseased neurons in tissue resected for epilepsy treatment from TSC and FCDII patients. Finally, blocking HCN4 channel activity in FCM neurons prevented epilepsy in mice. These findings that demonstrate HCN4 acquisition as seizure-genic, identify a novel cAMP-dependent seizure mechanism in TSC and FCDII. Furthermore, the unique expression of HCN4 exclusively in FCM neurons provides opportunities for using HCN4 as a gene therapy target to treat epilepsy in individuals with FCDII or TSC.One Sentence SummaryOur data provide a novel cAMP-dependent mechanism of seizure initiation in focal cortical dysplasia and tuberous sclerosis complex due to the unexpected ectopic expression of HCN4 channels only in diseased neurons. HCN4 channels are thus promising candidates for gene therapy to treat epilepsy generated by mTOR-driven focal malformations.
Face familiarity detection with complex synapses
Authors: Ji-An Li , Stefanini Fabio , Benna Marcus K. , Fusi Stefano 
Published: November 2019

AbstractSynaptic plasticity is a complex phenomenon involving multiple biochemical processes that operate on different timescales. We recently showed that this complexity can greatly increase the memory capacity of neural networks when the variables that characterize the synaptic dynamics have limited precision, as in biological systems. These types of complex synapses have been tested mostly on simple memory retrieval problems involving random and uncorrelated patterns. Here we turn to a real-world problem, face familiarity detection, and we show that also in this case it is possible to take advantage of synaptic complexity to store in memory a large number of faces that can be recognized at a later time. In particular, we show that the familiarity memory capacity of a system with complex synapses grows almost linearly with the number of the synapses and quadratically with the number of neurons. Complex synapses are superior to simple ones, which are characterized by a single variable, even when the total number of dynamical variables is matched. We further show that complex and simple synapses have distinct signatures that are testable in proposed experiments. Our results indicate that a memory system with complex synapses can be used in real-world tasks such as face familiarity detection.SignificanceThe complexity of biological synapses is probably important for enabling us to remember the past for a long time and rapidly store new memories. The advantage of complex synapses in terms of memory capacity is significant when the variables that characterize the synaptic dynamics have limited precision. This advantage has been estimated under the simplifying assumption that the memories to be stored are random and uncorrelated. Here we show that synaptic complexity is important also in a more challenging and realistic face familiarity detection task. We built a simple neural circuit that can report whether a face has been previously seen or not. This circuit incorporates complex synapses that operate on multiple timescales. The memory performance of this circuit is significantly higher than in the case in which synapses are simple, indicating that the complexity of biological synapses can be important also in real-world memory tasks.
Combined use of metagenomic sequencing and host response profiling for the diagnosis of suspected sepsis
Authors: Cheng Henry K. , Tan Susanna K. , Sweeney Timothy E. , Jeganathan Pratheepa , Briese Thomas , Khadka Veda , Strouts Fiona , Thair Simone , Dalai Sudeb , Hitchcock Matthew , Multani Ashrit , Aronson Jenny , Andermann Tessa , Yu Alexander , Yang Samuel , Holmes Susan P. , Lipkin W. Ian , Khatri Purvesh , Relman David A. 
Published: November 2019

ABSTRACTBackgroundCurrent diagnostic techniques are inadequate for rapid microbial diagnosis and optimal management of patients with suspected sepsis. We assessed the clinical impact of three powerful molecular diagnostic methods.MethodsWith blood samples from 200 consecutive patients with suspected sepsis, we evaluated 1) metagenomic shotgun sequencing together with a Bayesian inference approach for contaminant sequence removal, for detecting bacterial DNA; 2) viral capture sequencing; and 3) transcript-based host response profiling for classifying patients as infected or not, and if infected, with bacteria or viruses. We then evaluated changes in diagnostic decision-making among three expert physicians by unblinding the results of these methods in a staged fashion.ResultsMetagenomic shotgun sequencing confirmed positive blood culture results in 14 of 26 patients. In 17 of 200 patients, metagenomic sequencing and viral capture sequencing revealed organisms that were 1) not detected by conventional hospital tests within 5 days after presentation, and 2) classified as of probable clinical relevance by physician consensus. Host response profiling led at least two of three physicians to change their diagnostic decisions in 46 of 100 patients. The data suggested possible bacterial DNA translocation in 8 patients who were originally classified by physicians as noninfected and illustrate how host response profiling can guide interpretation of metagenomic shotgun sequencing results.ConclusionsThe integration of host response profiling, metagenomic shotgun sequencing, and viral capture sequencing enhances the utility of each, and may improve the diagnosis and management of patients with suspected sepsis.
Organizational learning capability, innovation and organizational performance
Authors: Migdadi Mahmoud M. 
Published: November 2019

PurposeThe purpose of this paper is to introduce a comprehensive, delineated and integrated conceptual model which includes organizational learning capability, innovation and organizational performance (OP). Then, an empirical investigation is undertaken to test the relationships among the proposed study model variables.Design/methodology/approachIn total, 274 questionnaires were completed and returned. Statistical techniques employed included confirmatory factor analysis to examine the validity of the measurement model, and structural equation modeling to test the hypotheses.FindingsThe findings of this study suggest that OLC influences innovation and innovation affects OP. Finally, the results show that OLC affects OP indirectly through innovation (mediator).Research limitations/implicationsFuture research should pay more attention to the influence of different mixture (variables) of influences on innovation and also examine other consequences of introducing innovation in organizations. In addition, more empirical papers supporting (or rejecting) the results in different contexts would be welcomed, especially longitudinal studies.Practical implicationsThe results of this study help managers to ascertain the managerial practices that can be employed as well as determine the level of effort and resources necessary to enhance OLC. Additionally, managers should shed additional light on the innovation’s positive implications for OP.Originality/valueThis study focuses on the conceptualization of OLC and effects of these capabilities on innovation. It conceptualizes innovation as a multidimensional construct and tests its relationship with OP. Finally, the relationship between learning capability and OP, although implied, needs to be addressed empirically in the research literature, an objective that this study tries to achieve.
Decision making under uncertainty in the alarm systems response
Authors: Si Mohammed Antar , Smail Rachid , Chebila Mourad 
Published: November 2019

Purpose
The purpose of this paper is to develop an advanced decision-making support for the appropriate responding to critical alarms in the hazardous industrial facilities.

Design/methodology/approach
A fuzzy analytical hierarchy process is suggested by considering three alternatives and four criteria using triangular fuzzy numbers to handle the associated uncertainty. A logarithmic fuzzy preference programming (LFPP)-based nonlinear priority method is employed to analyze the suggested model.

Findings
A quantitative decision-making support is not only a necessity in responding to critical alarms but also easy to implement even in a relatively short reaction time. Confirmation may not be the appropriate option to deal with a critical alarm, even with the availability of the needed resources.

Practical implications
A situation related to a flammable gas alarm in a gas plant is treated using the developed model showing its practical efficiency and practicality.

Originality/value
The proposed model provides a rational, simple and holistic fuzzy multi criteria tool with a refined number of criteria and alternatives using an LFPP method to handle process alarms.
Tourist experience, perceived authenticity, place attachment and loyalty when staying in a peer-to-peer accommodation
Authors: Souza Luis Henrique , Kastenholz Elisabeth , Barbosa Maria de Lourdes Azevedo , Carvalho Mariana Sousa e Silva Cabral 
Published: November 2019

PurposeThe emergence of peer-to-peer accommodation (P2PA) introduces new values and meanings to the hospitality experience. Focusing on the diverse dimensions of the tourist experience, the purpose of this paper is to identify and assess the relative importance of the main dimensions of guests’ P2PA experience and its relationships with perception of authenticity, place attachment and loyalty to both the visited destination and the P2PA.Design/methodology/approachA qualitative netnographic approach with content analysis permitted the analysis of 250 reviews taken from the Airbnb platform, specifically focusing on P2PAs where guests stay with hosts in the same space.FindingsThe results of the study suggest that guests’ P2PA experiences are particularly influenced by the experience dimensions “aesthetic/sense”, “relate/social interaction”, “escape”, “act” and “feel”. P2PA experiences also result in loyalty intentions, to both the visited destination and the particular P2PA. The dimensions “aesthetic/sense”, “relate/social interaction” and “escape” stand out as most influential in determining perceived authenticity. In turn, place attachment is most influenced by the dimensions “feel” and “relate/social interaction”.Research limitations/implicationsLimitations of this research need to be acknowledged: the P2PA guest experience is explored from the restricted perspective of online reviews using passive netnography. Therefore, some criteria of data collection, for instance, gathering only reviews written in English and with more than 80 words, may be limitative in a more comprehensive assessment of the P2PA experience. Another point is, although P2PA platforms such as Airbnb encourage their guests to review the experience, some people are not inclined to do so; therefore, the published reviews may not reflect all possible experiences at these accommodations inclined to do so; therefore, the published reviews may not reflect all possible experiences at these accommodations.Originality/valueThis study suggests a comprehensive analytical framework for assessing the “holistic multidimensional tourist experience”, integrating Pine and Gilmore’s (1999) and Schmitt’s (1999) approaches, thus deepening the conceptual and methodological debate on the tourist experience. It further contributes to a better understanding of the dimensionality of the tourist experience in the context of shared accommodation. The dimensions under analysis and their association with perceived authenticity, loyalty and place attachment are both of theoretical and practical interest, suggesting approaches to improve the P2PA experience as well as the image and success of the destinations where these units are located.
Impact of anchor investors on IPO returns during pre-market and aftermarket: evidence from India
Authors: Gupta Vikas , Singh Shveta , Yadav Surendra S. 
Published: November 2019

Purpose
The unique regulatory design of India provides us with the opportunity to disaggregate traditional initial public offering (IPO) underpricing into three categories: voluntary, pre-market and post-market. The presence of anchor investors in India makes it a compelling case to study. These individuals were introduced to bring transparency in the book building process, but their impact on pre-market and post-market underpricing was not foreseen. Therefore, the purpose of this paper is to evaluate the impact of anchor investors on the IPO underpricing after disaggregation and on the long-run performance of an IPO.

Design/methodology/approach
A sample covering 232 IPOs from a period of 2009–2018 is included. The empirical analysis explores the impact of various firm-specific as well as market-specific variables on IPO underpricing. The financial data for the empirical analysis are extracted from Prime database and websites of National Stock Exchange and Bombay Stock Exchange. To deal with the outliers effectively, this paper deploys “robust-regression.”

Findings
The study finds that investor’s subscription rate and voluntary underpricing impacts the pre-market but do not have any impact on the post-market while the age of the firm has a different impact on both the markets and the number of anchor investors have the same impact in both markets. Anchor investors’ participation increases the pre-market as well as post-market underpricing. Lastly, the long-term performance of IPOs backed by the anchor investors is high relative to the IPOs not subscribed to by the anchor investors.

Originality/value
This paper is believed to be the first attempt to study the impact of anchor investors on the disaggregated IPO underpricing. The findings of this study will have a great insight for the investors.