bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reducing Length of Stay after Microsurgical Breast Reconstruction with a Standardized Postoperative Protocol
Authors: DelMauro Matthew A. , Chen Kevin , Keller Alex 
Published: May 2019

Abstract
Background Despite widespread acceptance of enhanced recovery after surgery protocols in other surgical specialties, plastic surgery has been slow to adopt fast-track principles. Recently, however, studies have shown that patients undergoing microsurgical breast reconstruction may benefit from a comprehensive postoperative protocol.
Methods All microsurgical breast reconstructions with abdominal free flaps performed by the senior author (A.K.) at a single institution from June 2009 to December 2013 were reviewed. Demographic information (e.g., age, body mass index, and comorbidities), operative details (e.g., laterality, type of flap), and postoperative data (e.g., complications, length of stay) were collected from patients' medical records. The authors employed a universal comprehensive protocol that dictated all postoperative care as it relates to diet, ambulation, flap monitoring, anticoagulation, analgesia, venous thromboembolism, antibiotic prophylaxis, and discharge criteria.
Results During the study period, 161 patients underwent 289 free flaps. The average length of stay for all patients was 3.26 ± 1.19 days. The incidence of complications requiring return to the operating room was 4.35% (7 patients). The incidence of flap failure was 0.69% (2 of 289 flaps). Only one flap failure occurred after hospital discharge. Statistical analysis demonstrated that the presence of any complication requiring return to the operating room increased hospital course by an average of 1.37 days (p = 0.0027).
Conclusion The standardization of postoperative care for patients undergoing microsurgical breast reconstruction results in a short hospital length of stay without increasing the incidence of flap failure or postoperative complications requiring return to the operating room.
Cell contact and Nf2/Merlin-dependent regulation of TEAD palmitoylation and activity
Authors: Kim Nam-Gyun , Gumbiner Barry M. 
Published: May 2019

Significance
The Hippo signaling pathway regulates cell proliferation in response to cell contact and a variety of other extracellular stimuli. It controls the activity and nuclear localization of cotranscriptional activator YAP, which interacts with DNA binding transcription factor TEAD, for the expression of target genes involved in cell proliferation. We show here that the expression level and transcriptional activity of TEAD are actively controlled by cell density through the modulation of its palmitoylation status. TEAD palmitoylation is controlled via fatty acid synthase and depalmitoylases in response to cell density. Our study indicates that the regulation of palmitoylation status is a potential target for controlling TEAD-dependent processes, perhaps including cancer growth.
Indigenous knowledge networks in the face of global change
Authors: Cámara-Leret Rodrigo , Fortuna Miguel A. , Bascompte Jordi 
Published: May 2019

SignificanceThe knowledge of nonliterate societies may vanish in silence jeopardizing indigenous peoples’ livelihoods. Yet, this cultural component is missed by studies on ecosystem services that have historically emphasized the biological dimension. Here we fill this gap by introducing indigenous knowledge networks representing the wisdom of indigenous people on plant species and the services they provide. This approach allows us to assess how knowledge held by 57 Neotropical indigenous communities is structured locally and regionally, how it is influenced by turnover in biological and cultural heritage, and how the progressive loss of biocultural heritage may undermine the resilience of these communities.
Impact of fast ions on density peaking in JET: fluid and gyrokinetic modeling
Authors: Eriksson F , Oberparleiter M , Skyman A , Nordman H , Strand P , Salmi A , Tala T 
Published: May 2019

Abstract
The effect of fast ions on turbulent particle transport, driven by ion temperature gradient (ITG)/trapped electron mode turbulence, is studied. Two neutral beam injection (NBI) heated JET discharges in different regimes are analyzed at the radial position ρ

t
= 0.6, one of them an L-mode and the other one an H-mode discharge. Results obtained from the computationally efficient fluid model EDWM and the gyro-fluid model TGLF are compared to linear and nonlinear gyrokinetic GENE simulations as well as the experimentally obtained density peaking. In these models, the fast ions are treated as a dynamic species with a Maxwellian background distribution. The dependence of the zero particle flux density gradient (peaking factor) on fast ion density, temperature and corresponding gradients, is investigated. The simulations show that the inclusion of a fast ion species has a stabilizing influence on the ITG mode and reduces the peaking of the main ion and electron density profiles in the absence of sources. The models mostly reproduce the experimentally obtained density peaking for the L-mode discharge whereas the H-mode density peaking is significantly underpredicted, indicating the importance of the NBI particle source for the H-mode density profile.
Topological time crystals
Authors: Giergiel Krzysztof , Dauphin Alexandre , Lewenstein Maciej , Zakrzewski Jakub , Sacha Krzysztof 
Published: May 2019

Abstract
By analogy with the formation of space crystals, crystalline structures can also appear in the time domain. While in the case of space crystals we often ask about periodic arrangements of atoms in space at a moment of a detection, in time crystals the role of space and time is exchanged. That is, we fix a space point and ask if the probability density for detection of a system at this point behaves periodically in time. Here, we show that in periodically driven systems it is possible to realize topological insulators, which can be observed in time. The bulk-edge correspondence is related to the edge in time, where edge states localize. We focus on two examples: Su-Schrieffer-Heeger model in time and Bose Haldane insulator which emerges in the dynamics of a periodically driven many-body system.
The Coordinated Universal Time (UTC)
Authors: Panfilo G , Arias F 
Published: May 2019

Abstract
Coordinated Universal Time (UTC) has considerably changed in recent years. The evolution of UTC follows the scientific and industrial progress by developing appropriate models, more adapted calculation algorithms, more efficient and rapid dissemination processes and a well defined traceability chain. The enormous technical progress worldwide has resulted in an impressive number of atomic clocks now available for UTC calculation. The refined time and frequency transfer techniques are approaching the accuracy requested for the new definition of the SI second. The more regular operation of primary frequency standards (PFS) increases the accuracy of UTC and opens a possible new development for time scale algorithms. From the metrological point of view all the ingredients are available for major improvements to UTC. Dissemination of UTC is done by the monthly publication of results in BIPM Circular T. This document makes a quality evaluation of local representations of UTC, named UTC(k), in national institutes, and other organizations, by giving the evolution of their offsets relative to UTC and their respective uncertainties. The clock models adopted and the time transfer techniques have progressively improved over the years, assuring the long-term stability of UTC. Each computation of UTC processes data over one month with five-day sampling and publication. A rapid solution of UTC (UTCr) has existed since 2013, and consists of the processing of daily sampled data over four consecutive weeks, computed and published weekly. It gives quick access to UTC, and allows participating laboratories to better monitor the offsets of their realizations to the reference UTC. The traditional monthly publication, containing results of all the laboratories contributing data to the BIPM for the computation of UTC was complemented after the establishment of the Mutual Recognition Arrangement of the International Committee on Weights and Measures (CIPM MRA). This time comparison, which has been the responsibility of the BIPM since 1988, added as a complement the key comparison on time defined by the Consultative Committee for Time and Frequency (CCTF) in 2006 as CCTF-K001.UTC, where the results published are those of national metrology institutes (NMIs) signatories of the CIPM MRA, or designated institutes (DIs). The traceability issues are formalized in the framework of the CIPM MRA. The development of time metrology activities in the different metrology regions, supports the actions of the BIPM time department to improve the accuracy of [UTC–UTC(k)], where the coordination with the Regional Metrology Organizations (RMOs) has a key role. This paper presents an overview of UTC.
SpikeDeeptector: a deep-learning based method for detection of neural spiking activity
Authors: Saif-ur-Rehman Muhammad , Lienkämper Robin , Parpaley Yaroslav , Wellmer Jörg , Liu Charles , Lee Brian , Kellis Spencer , Andersen Richard , Iossifidis Ioannis , Glasmachers Tobias , Klaes Christian 
Published: May 2019

Abstract

Objective. In electrophysiology, microelectrodes are the primary source for recording neural data (single unit activity). These microelectrodes can be implanted individually or in the form of arrays containing dozens to hundreds of channels. Recordings of some channels contain neural activity, which are often contaminated with noise. Another fraction of channels does not record any neural data, but only noise. By noise, we mean physiological activities unrelated to spiking, including technical artifacts and neural activities of neurons that are too far away from the electrode to be usefully processed. For further analysis, an automatic identification and continuous tracking of channels containing neural data is of great significance for many applications, e.g. automated selection of neural channels during online and offline spike sorting. Automated spike detection and sorting is also critical for online decoding in brain–computer interface (BCI) applications, in which only simple threshold crossing events are often considered for feature extraction. To our knowledge, there is no method that can universally and automatically identify channels containing neural data. In this study, we aim to identify and track channels containing neural data from implanted electrodes, automatically and more importantly universally. By universally, we mean across different recording technologies, different subjects and different brain areas. Approach. We propose a novel algorithm based on a new way of feature vector extraction and a deep learning method, which we call SpikeDeeptector. SpikeDeeptector considers a batch of waveforms to construct a single feature vector and enables contextual learning. The feature vectors are then fed to a deep learning method, which learns contextualized, temporal and spatial patterns, and classifies them as channels containing neural spike data or only noise. Main results. We trained the model of SpikeDeeptector on data recorded from a single tetraplegic patient with two Utah arrays implanted in different areas of the brain. The trained model was then evaluated on data collected from six epileptic patients implanted with depth electrodes, unseen data from the tetraplegic patient and data from another tetraplegic patient implanted with two Utah arrays. The cumulative evaluation accuracy was 97.20% on 1.56 million hand labeled test inputs. Significance. The results demonstrate that SpikeDeeptector generalizes not only to the new data, but also to different brain areas, subjects, and electrode types not used for training. Clinical trial registration number. The clinical trial registration number for patients implanted with the Utah array is NCT 01849822. For the epilepsy patients, approval from the local ethics committee at the Ruhr-University Bochum, Germany, was obtained prior to implantation.
Epidural recordings in cochlear implant users
Authors: Haumann S , Bauernfeind G , Teschner M J , Schierholz I , Bleichner M G , Büchner A , Lenarz T 
Published: May 2019

Abstract

Objective. In the long term it is desirable for CI users to control their device via brain signals. A possible strategy is the use of auditory evoked potentials (AEPs). Several studies have shown the suitability of auditory paradigms for such an approach. However, these investigations are based on non-invasive recordings. When thinking about everyday life applications, it would be more convenient to use implanted electrodes for signal acquisition. Ideally, the electrodes would be directly integrated into the CI. Further it is to be expected that invasively recorded signals have higher signal quality and are less affected by artifacts. Approach. In this project we investigated the feasibility of implanting epidural electrodes temporarily during CI surgery and the possibility to record AEPs in the course of several days after implantation. Intraoperatively, auditory brainstem responses were recorded, whereas various kinds of AEPs were recorded postoperatively. After a few days the epidural electrodes were removed. Main results. Data sets of ten subjects were obtained. Invasively recorded potentials were compared subjectively and objectively to clinical standard recordings using surface electrodes. Especially the cortical evoked response audiometry depicted clearer N1 waves for the epidural electrodes which were also visible at lower stimulation intensities compared to scalp electrodes. Furthermore the signal was less disturbed by artifacts. The objective quality measure (based on data sets of six patients) showed a significant better signal quality for the epidural compared to the scalp recordings. Significance. Altogether the approach revealed to be feasible and well tolerated by the patients. The epidural recordings showed a clearly better signal quality than the scalp recordings with AEPs being clearer recognizable. The results of the present study suggest that including epidural recording electrodes in future CI systems will improve the everyday life applicability of auditory closed loop systems for CI subjects.
Projected precipitation changes over the south Asian region for every 0.5 °C increase in global warming
Authors: Bhowmick Mansi , Sahany Sandeep , Mishra Saroj K 
Published: May 2019

Abstract
Using all ensemble members of NCAR CCSM4 for historical natural, RCP4.5 and RCP8.5 scenarios from CMIP5, we analyse changes in mean and extreme precipitation over the south Asian region for every 0.5 oC increase in global warming. An increase in mean annual precipitation is projected over majority of the south Asian region with increased levels of warming. Over Indian land, the spatially-averaged annual mean precipitation shows an increase in the range of ~2-14 % based on the RCP scenario and level of warming. However, a decrease in mean annual precipitation is projected over northwest parts of the Indian sub-continent and the equatorial Indian Ocean with increased levels of warming. In general, we find multifold increase in the frequency of occurrence of daily precipitation extremes over the Indian subcontinent and surrounding oceans. Over Indian land, frequency of occurrence of daily precipitation extremes show up to three-fold increase under both RCP scenarios for global warming levels in the range of 1.5 oC–2.5 oC. With further increase in warming we find that the frequency of occurrence of daily precipitation extremes could show a massive four- to six-fold increase over majority of Indian land. Notably, unlike the projected increase in the frequency of occurrence of daily precipitation extremes, the projected change in annual mean precipitation is found to be insignificant in a 1.5 oC warmer world, over majority of the south Asian region, under both RCP scenarios. Given the projected large increase in frequency of daily precipitation extremes with increased levels of warming, our study provides scientific support to the recommendations of the Paris Agreement of 2015.
Crude Protein, Amino Acid, and Iron Content of Tenebrio molitor (Coleoptera, Tenebrionidae) Reared on an Agricultural Byproduct from Maize Production: An Exploratory Study
Authors: Stull Valerie J , Kersten Marjorie , Bergmans Rachel S , Patz Jonathan A , Paskewitz Susan 
Published: May 2019

Abstract
Edible insects offer environmental and nutritional benefits, as they are characteristically nutrient-dense, are efficient biotransformers of organic material, and emit fewer greenhouse gasses than traditional livestock. Cultivating Tenebrio molitor (yellow mealworm) as ‘minilivestock’ is one possible means of increasing access to insect protein for food insecure populations. Tenebrio molitor growth and nutrient content varies with diet and rearing conditions, but little is known about the precise impact of poor quality feedstocks, such as maize crop residue (stover). Stover is widely available across sub-Saharan Africa where maize is a common dietary staple. Early instar larvae were reared under controlled conditions on three feed substrates: a standard control; a mixed soy, maize grain, and stover diet; and a 100% stover diet. Larvae reared for 32 d were analyzed for total amino acid profile, crude protein, and iron content. Larvae fed the three diets contained all essential amino acids for human nutrition and compared favorably to other traditional protein sources. The mixed diet contained 40% stover by weight and yielded amino acid values similar to the control diet, suggesting that some grain feedstock could be replaced with stover without hampering nutrient content. A second experiment demonstrated that T. molitor were able to complete metamorphosis and survive on a 100% stover diet for multiple generations. These results suggest that stover could be a suitable dietary component for T. molitor, which could facilitate the development of low-cost insect farming systems in low-resource settings that stand to benefit from increased access nutrient-dense edible insects.
An Area-Level Indicator of Latent Soda Demand: Spatial Statistical Modeling of Grocery Store Transaction Data to Characterize the Nutritional Landscape in Montreal, Canada
Authors: Mamiya Hiroshi , Schmidt Alexandra M , Moodie Erica E M , Ma Yu , Buckeridge David L 
Published: May 2019

AbstractMeasurement of neighborhood dietary patterns at high spatial resolution allows public health agencies to identify and monitor communities with an elevated risk of nutrition-related chronic diseases. Currently, data on diet are obtained primarily through nutrition surveys, which produce measurements at low spatial resolutions. The availability of store-level grocery transaction data provides an opportunity to refine the measurement of neighborhood dietary patterns. We used these data to develop an indicator of area-level latent demand for soda in the Census Metropolitan Area of Montreal in 2012 by applying a hierarchical Bayesian spatial model to data on soda sales from 1,097 chain retail food outlets. The utility of the indicator of latent soda demand was evaluated by assessing its association with the neighborhood relative risk of prevalent type 2 diabetes mellitus. The indicator improved the fit of the disease-mapping model (deviance information criterion: 2,140 with the indicator and 2,148 without) and enables a novel approach to nutrition surveillance.
Prediction of tumor metastasis from sequencing data in the era of genome sequencing
Authors: Yuan Linlin , Guo Fei , Wang Lei , Zou Quan 
Published: May 2019

AbstractTumor metastasis is the key reason for the high mortality rate of tumor. Growing number of scholars have begun to pay attention to the research on tumor metastasis and have achieved satisfactory results in this field. The advent of the era of sequencing has enabled us to study cancer metastasis at the molecular level, which is essential for understanding the molecular mechanism of metastasis, identifying diagnostic markers and therapeutic targets and guiding clinical decision-making. We reviewed the metastasis-related studies using sequencing data, covering detection of metastasis origin sites, determination of metastasis potential and identification of distal metastasis sites. These findings include the discovery of relevant markers and the presentation of prediction tools. Finally, we discussed the challenge of studying metastasis considering the difficulty of obtaining metastatic cancer data, the complexity of tumor heterogeneity and the uncertainty of sample labels.
Machine learning and statistical methods for clustering single-cell RNA-sequencing data
Authors: Petegrosso Raphael , Li Zhuliu , Kuang Rui 
Published: May 2019

Abstract

Single-cell RNAsequencing (scRNA-seq) technologies have enabled the large-scale whole-transcriptome profiling of each individual single cell in a cell population. A core analysis of the scRNA-seq transcriptome profiles is to cluster the single cells to reveal cell subtypes and infer cell lineages based on the relations among the cells. This article reviews the machine learning and statistical methods for clustering scRNA-seq transcriptomes developed in the past few years. The review focuses on how conventional clustering techniques such as hierarchical clustering, graph-based clustering, mixture models, $k$-means, ensemble learning, neural networks and density-based clustering are modified or customized to tackle the unique challenges in scRNA-seq data analysis, such as the dropout of low-expression genes, low and uneven read coverage of transcripts, highly variable total mRNAs from single cells and ambiguous cell markers in the presence of technical biases and irrelevant confounding biological variations. We review how cell-specific normalization, the imputation of dropouts and dimension reduction methods can be applied with new statistical or optimization strategies to improve the clustering of single cells. We will also introduce those more advanced approaches to cluster scRNA-seq transcriptomes in time series data and multiple cell populations and to detect rare cell types. Several software packages developed to support the cluster analysis of scRNA-seq data are also reviewed and experimentally compared to evaluate their performance and efficiency. Finally, we conclude with useful observations and possible future directions in scRNA-seq data analytics.

Availability
All the source code and data are available at https://github.com/kuanglab/single-cell-review.