bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spike sorting: new trends and challenges of the era of high-density probes
Authors: Buccino Alessio P , Garcia Samuel , Yger Pierre 
Published: April 2022

Abstract
Recording from a large neuronal population of neurons is a crucial challenge to unravel how information is processed by the brain. In this review, we highlight the recent advances made in the field of ‘spike sorting’, which is arguably a very essential processing step to extract neuronal activity from extracellular recordings. More specifically, we target the challenges faced by newly manufactured high-density multi-electrode array devices (HD-MEA), e.g. Neuropixels probes. Among them, we cover in depth the prominent problem of drifts (movements of the neurons with respect to the recording devices) and the current solutions to circumscribe it. In addition, we also review recent contributions making use of deep learning approaches for spike sorting, highlighting their advantages and disadvantages. Next, we highlight efforts and advances in unifying, validating, and benchmarking spike sorting tools. Finally, we discuss the spike sorting field in terms of its open and unsolved challenges, specifically regarding scalability and reproducibility. We conclude by providing our personal view on the future of spike sorting, calling for a community-based development and validation of spike sorting algorithms and fully automated, cloud-based spike sorting solutions for the neuroscience community.
Bio-inspired navigation and exploration system for a hexapod robotic platform
Authors: Pardo-Cabrera Josh , Rivero-Ortega Jesús D , Hurtado-López Julián , Ramírez-Moreno David F 
Published: April 2022

Abstract
This paper presents a biologically inspired system for guiding and controlling a virtual hexapod robot. Our navigation and exploration system is composed of subsystems that execute processes of path integration, action selection, actuator control and correction of the robot’s orientation. For the subsystem that serves the path integration function we modified an existing model of bio-inspired vector summation by adding the capability of performing online calculation. For the action selection subsystem that allows to switch between the behaviors of exploration, approaching a target and homing we modified an existing model of decision making for mediating social behaviors in mice. We added an additional circuit that projects a signal to the units representing each of the behaviors. In the case of the actuator control subsystem, the structure of a central pattern generator model that incorporates feedback and adaptation was used as the base for generating and transforming signals for the actuators. Finally, the orientation correction subsystem is a novel model that determines an error value from a desired and the current orientations. The proposed models were simulated as independent scripts and then implemented as ROS (Robot Operating System) nodes for controlling a robot simulation in Gazebo.
Scaling of voltage controlled magnetic anisotropy based skyrmion memory and its neuromorphic application
Authors: Akanda Md Rakibul Karim 
Published: April 2022

Abstract
Voltage controlled skyrmion memory requires less energy compared to current controlled method where voltage changes magnetic anisotropy (VCMA) and Dzyaloshinskii-Moriya interaction (DMI). Ferromagnetic (FM) and synthetic antiferromagnetic (SAFM) memory devices are simulated using electric field control method where gate and gap width are chosen as smaller than skyrmion size so that skyrmion can feel the change in voltage polarity in the neighbouring gate and moves accordingly. Scaling of memory device is performed which shows SAFM memory can be made much narrower compared to FM memory as skyrmion diameter also depends on width of the structure. Effects of device structure and skyrmion-skyrmion repulsion force on skyrmion diameter variation are shown in cylindrical structure considering effect of demagnetizing field. Apart from these, neuromorphic application is considered where skyrmion moves from central square neuron region to surrounding synapse region or vice versa by the application of voltage. Switching time, voltage range, energy and scaling of device dimensions are shown for synapse-neuron having different number of skyrmions where multiple skyrmions represent different weight in the neuromorphic circuit.
A model to determine soiling, shading and thermal losses from PV yield data
Authors: Ghosh S , Roy J N , Chakraborty C 
Published: April 2022

Abstract
Apart from being a clean source of energy, photovoltaic (PV) power plants are also a source of income generation for its investors and lenders. Therefore, mitigation of system losses is crucial for economic operation of PV plants. Combined losses due to soiling, shading and temperature in PV plants go as high as 50%. Much of these losses are unaccounted initially, which can jeopardize the economic viability of PV projects. This paper aims to provide a model to determine losses due to soiling, shading and temperature using quantities like irradiance, cell temperature, DC power and current, which are readily available in PV yield data captured by the remote monitoring system, without involving any additional sensors or equipment. In this study, soiling, shading and thermal losses were calculated using PV yield data obtained from a 30-kWp PV plant located in Kharagpur, India. The results showed soiling and shading losses as high as 25.7% and 9.7%, respectively, in the month of December. Soiling loss was verified by measuring transmittance loss of coupon glasses installed in the vicinity of the plant. Shading loss was verified by shadow simulation using an architectural tool (SketchUp). Array thermal loss obtained using the proposed methodology was found to be in line with the estimated value obtained from PVsyst simulation. Additionally, using time-series data, the energy losses corresponding to soiling, shading and temperature effects were calculated by a numerical-integration technique. The monetary loss due to these energy losses thus obtained provides criteria for deciding when to mitigate the sources of these losses.
Hidden in plain sight: challenges in proteomics detection of small ORF-encoded polypeptides
Authors: Fijalkowski Igor , Willems Patrick , Jonckheere Veronique , Simoens Laure , Van Damme Petra 
Published: April 2022

AbstractGenomic studies of bacteria have long pointed toward widespread prevalence of small open reading frames (sORFs) encoding for short proteins, &lt;100 amino acids in length. Despite the mounting genomic evidence of their robust expression, relatively little progress has been made in their mass spectrometry-based detection and various blanket statements have been used to explain this observed discrepancy. In this study, we provide a large-scale riboproteogenomics investigation of the challenging nature of proteomic detection of such small proteins as informed by conditional translation data. A panel of physiochemical properties alongside recently developed mass spectrometry detectability metrics was interrogated to provide a comprehensive evidence-based assessment of sORF-encoded polypeptide (SEP) detectability. Moreover, a large-scale proteomics and translatomics compendium of proteins produced by Salmonella Typhimurium (S. Typhimurium), a model human pathogen, across a panel of growth conditions is presented and used in support of our in silico SEP detectability analysis. This integrative approach is used to provide a data-driven census of small proteins expressed by S. Typhimurium across growth phases and infection-relevant conditions. Taken together, our study pinpoints current limitations in proteomics-based detection of novel small proteins currently missing from bacterial genome annotations.
The dynamic effect of genetic variation on the in vivo ER stress transcriptional response in different tissues
Authors: Russell Nikki D , Chow Clement Y 
Published: April 2022

Abstract
The genetic regulation of gene expression varies greatly across tissue-type and individuals and can be strongly influenced by the environment. Many variants, under healthy control conditions, may be silent or even have the opposite effect under diseased stress conditions. This study uses an in vivo mouse model to investigate how the effect of genetic variation changes with cellular stress across different tissues. Endoplasmic reticulum stress occurs when misfolded proteins accumulate in the endoplasmic reticulum. This triggers the unfolded protein response, a large transcriptional response which attempts to restore homeostasis. This transcriptional response, despite being a conserved, basic cellular process, is highly variable across different genetic backgrounds, making it an ideal system to study the dynamic effects of genetic variation. In this study, we sought to better understand how genetic variation alters expression across tissues, in the presence and absence of endoplasmic reticulum stress. The use of different mouse strains and their F1s allow us to also identify context-specific cis- and trans- regulatory variation underlying variable transcriptional responses. We found hundreds of genes that respond to endoplasmic reticulum stress in a tissue- and/or genotype-dependent manner. The majority of the regulatory effects we identified were acting in cis-, which in turn, contribute to the variable endoplasmic reticulum stress- and tissue-specific transcriptional response. This study demonstrates the need for incorporating environmental stressors across multiple different tissues in future studies to better elucidate the effect of any particular genetic factor in basic biological pathways, like the endoplasmic reticulum stress response.
Age and Physical Activity Levels in Companion Dogs: Results From the Dog Aging Project
Authors: Lee Hannah , Collins Devin , Creevy Kate E , Promislow Daniel E L ,   Dog Aging Project Consortium, Akey Joshua M , Benton Brooke , Borenstein Elhanan , Castelhano Marta G , Coleman Amanda E , Creevy Kate E , Crowder Kyle , Dunbar Matthew D , Fajt Virginia R , Fitzpatrick Annette L , Jeffery Unity , Jonlin Erica C , Kaeberlein Matt , Karlsson Elinor K , Kerr Kathleen F , Levine Jonathan M , Ma Jing , McClelland Robyn L , Promislow Daniel E L , Ruple Audrey , Schwartz Stephen M , Shrager Sandi , Snyder-Mackler Noah , Tolbert Katherine , Urfer Silvan R , Wilfond Benjamin S 
Published: April 2022

AbstractWhile there has been an abundance of studies on the important relationship between physical activity and age in both dogs and humans, studies on dogs have primarily focused on how a dog’s biological characteristics, such as their weight, affect the age–activity relationship. To date, there is little knowledge about how this relationship may be associated with contextual- and owner-level characteristics. We leveraged a large and novel data set from the Dog Aging Project (DAP) to investigate the extent to which the age–activity relationship is associated with certain dog and owner characteristics, namely dog size, owner age, and the environment in which they live. Dogs are a unique model for aging research as they are exposed to similar social and environmental elements as humans but have a shorter life span, allowing researchers to observe their entire life course. We find that older dogs are less active than younger dogs; rural dogs are more active than suburban and urban dogs, especially at younger ages; and larger dogs are more active than smaller dogs. These findings are generally consistent with previous studies. However, a surprising finding is that older owners have more active dogs than younger owners. As one of the first studies to utilize the large survey data from the DAP, this study lays the foundation for future investigations to further understand and identify the biological, social, and environmental causes, as well as consequences, of aging.
Losartan Mitigates Oxidative Stress in the Brains of Aged and Inflamed IL-10−/− Mice
Authors: Saleh Nazaneen , Cosarderelioglu Caglar , Vajapey Ramya , Walston Jeremy , Abadir Peter M 
Published: April 2022

Abstract
Chronic inflammation, oxidative stress, and dysregulation of the renin–angiotensin system are closely linked, and their crosstalk commonly contributes to age-related physical and cognitive decline. The primary dementia-protective benefits of Angiotensin II type 1 receptor (AT1R) blockers are believed to arise from systemic effects on blood pressure. However, there is an independently regulated brain-specific renin–angiotensin system. Here, we examined the impact of 4 weeks of oral Losartan treatment on the brains of aged (100 weeks old) IL-10−/− mice, an animal model of chronic inflammation and frailty. Our data show that aged IL-10−/− mice have higher AT1R and Nitrotyrosine (oxidative stress marker) levels in their frontal cortex tissue but not in cerebellar or hippocampal tissue compared to age- and sex-matched wild type mice. Losartan treatment for 4 weeks is associated with lower AT1R protein level, Nitrotyrosine, and Tau protein in the frontal cortex of aged IL-10−/− mice. Our results highlight the impact of Losartan, an AT1R blocker commonly prescribed for treating high blood pressure, on the brain-specific angiotensin system and AT1R-linked downstream effects such as brain oxidative stress damage and Tau burden in a frailty mouse model.
Discrimination, Racial Identity, and Hypertension Among Black Americans Across Young, Middle, and Older Adulthood
Authors: Thomas Tobin Courtney S , Gutiérrez Ángela , Norris Keith C , Thorpe Roland J 
Published: April 2022

Abstract

Objectives
Substantial evidence documents the protective role of racial identity—or the meaning and significance that individuals attribute to race—among Black Americans, yet the impact of racial identity on physical health outcomes beyond young adulthood is unclear. To clarify the extent to which racial identity remains influential for physical health across the life course, this study investigated (a) the direct associations between discrimination, racial identity, and hypertension, (b) whether racial identity buffered the negative effects of discrimination, and (c) the extent to which these patterns varied among young (21–35), middle-aged (36–49), and older (&gt;50) Black adults.

Methods
Data from the Nashville Stress and Health Study (N = 627) were used to examine two identity dimensions: “racial centrality” (i.e., importance of Black identity to one’s sense of self) and “closeness to other Black people” (COBP). Modified Poisson models estimated relationships between racial identity, discrimination, and hypertension. Interactions determined whether racial identity moderated the discrimination–hypertension association within and across age groups.

Results
High centrality and moderate COBP were directly linked to elevated hypertension odds among young adults, but lower odds among older adults; racial identity was not directly associated with hypertension among middle-aged adults. Results also indicated that racial identity conditioned the discrimination–hypertension relationship in distinct ways across age groups.

Discussion
Findings underscore the significance of racial identity as sources of both psychosocial vulnerability and resilience for minority aging. Clinicians and public health professionals should consider racial identity beyond young adulthood to promote healthy aging via hypertension management among Black Americans.
Cohort Trends in the Burden of Multiple Chronic Conditions Among Aging U.S. Adults
Authors: Bishop Nicholas J , Haas Steven A , Quiñones Ana R 
Published: April 2022

Abstract

Objectives
Multimorbidity, also referred to as multiple chronic conditions (MCCs), is the concurrent presence of 2 or more chronic health conditions. Increasing multimorbidity represents a substantial threat to the health of aging populations. Recent trends suggest greater risk of poor health and mortality among later-born cohorts, yet we are unaware of work examining cohort differences in multimorbidity among aging U.S. adults.

Methods
We examine intercohort variation in MCC burden in adults aged 51 years and older using 20 years (n = 33,598; 1998–2018) of repeated assessment drawn from the Health and Retirement Study. The index of MCCs included 9 chronic conditions (heart disease, hypertension, stroke, diabetes, arthritis, lung disease, cancer excluding skin cancer, high depressive symptoms, and cognitive impairment). We used linear mixed models with various approaches to estimate age/period/cohort effects to model intercohort patterns in MCC burden. We also explored variation in the specific conditions driving cohort differences in multimorbidity.

Results
More recent cohorts had greater MCC burden and developed multimorbidity at earlier ages than those born to prior generations. The burden of chronic conditions was patterned by life-course sociodemographic factors and childhood health for all cohorts. Among adults with multimorbidity, arthritis and hypertension were the most prevalent conditions for all cohorts, and there was evidence that high depressive symptoms and diabetes contributed to the observed cohort differences in multimorbidity risk.

Discussion
Our results suggest increasing multimorbidity burden among more recently born cohorts of aging U.S. adults and should inform policy to address diminishing health in aging populations.
Identification of shared loci associated with both Crohn’s disease and leprosy in East Asians
Authors: Jung Seulgi , Park Dohoon , Lee Ho-Su , Kim Yongjae , Baek Jiwon , Hwang Sung Wook , Park Sang Hyoung , Yang Suk-Kyun , Ye Byong Duk , Han Buhm , Sun Yonghu , Liu Hong , Zhang Furen , Liu Jianjun , Song Kyuyoung 
Published: April 2022

Abstract
Genome-wide association studies (GWAS) of Crohn’s disease (CD) in European and leprosy in Chinese population have shown that CD and leprosy share genetic risk loci. As these shared loci were identified through cross-comparisons across different ethnic populations, we hypothesized that meta-analysis of GWAS on CD and leprosy in East Asian populations would increase power to identify additional shared loci. We performed a cross-disease meta-analysis of GWAS data from CD (1621 cases and 4419 controls) and leprosy (2901 cases 3801 controls) followed by replication in additional datasets comprising 738 CD cases and 488 controls and 842 leprosy cases and 925 controls. We identified one novel locus at 7p22.3, rs77992257 in intron 2 of ADAP1, shared between CD and leprosy with genome-wide significance (P = 3.80 × 10−11) and confirmed 10 previously established loci in both diseases: IL23R, IL18RAP, IL12B, RIPK2, TNFSF15, ZNF365-EGR2, CCDC88B, LACC1, IL27, NOD2. Phenotype variance explained by the polygenic risk scores derived from Chinese leprosy data explained up to 5.28% of variance of Korean CD, supporting similar genetic structures between the two diseases. Although CD and leprosy shared a substantial number of genetic susceptibility loci in East Asians, the majority of shared susceptibility loci showed allelic effects in the opposite direction. Investigation of the genetic correlation using cross-trait linkage disequilibrium score regression also showed a negative genetic correlation between CD and leprosy (rg [SE] = −0.40[0.13], P = 2.6 × 10−3). These observations implicate the possibility that CD might be caused by hyper-sensitive reactions toward pathogenic stimuli.
Evaluating the potential of lignosulfonates and chitosans as alfalfa hay preservatives using in vitro techniques
Authors: Leon-Tinoco Angela Y , Annis Seanna L , Almeida Saulo T , Guimarães Bianca C , Killerby Marjorie , Zhang Jinglin , Wu Changqing , Perkins Lewis B , Ma Zhengxin , Jeong Kwangcheol C , Romero Juan J 
Published: April 2022

Abstract
Our objectives were to compare the antifungal activity of 5 lignosulfonates, and 2 chitosans against fungi isolated from spoiled hay, and assess the effects of an optimized lignosulfonate, chitosan, and propionic acid (PRP) on high-moisture alfalfa hay. In experiment 1, we determined the minimum inhibitory concentration and minimum fungicidal concentration of 4 sodium lignosulfonates, 1 magnesium lignosulfonate, 2 chitosans, and PRP (positive control) against Aspergillus amoenus, Mucor circinelloides, Penicillium solitum, and Debaromyces hansenii at pH 4 and 6. Among sodium lignosulfonates, the one from Sappi Ltd. (NaSP) was the most antifungal at pH 4. However, chitosans had the strongest fungicidal activity with the exception of M. circinelloides at both pH 4 and 6. PRP had more antifungal effects than NaSP and was only better than chitosans for M. circinelloides. In experiment 2, we evaluated the effects of 3 additives (ADV): optimized NaSP (NaSP-O, UMaine), naïve chitosan (ChNv, Sigma–Aldrich), and PRP on high-moisture alfalfa hay. The experimental design was a randomized complete block design replicated 5 times. Treatment design was the factorial combination of 3 ADV× 5 doses (0, 0.25, 0.5, 1, and 2% w/w fresh basis). Additives were added to 35 g of sterile alfalfa hay (71.5 ± 0.23% DM), inoculated with a mixture of previously isolated spoilage fungi (5.8 log cfu/fresh g), and aerobically incubated in vitro for 23 d (25°C). After incubation, DM losses were reduced by doses as low as 0.25% for both NaSP-O and PRP (x¯=1.61) vs. untreated hay (24.0%), partially due to the decrease of mold and yeast counts as their doses increased. Also, hay NH3-N was lower in NaSP-O and PRP, with doses as low as 0.25%, relative to untreated hay (x¯=1.13 vs. 7.80% of N, respectively). Both NaSP-O and PRP increased digestible DM recovery (x¯=69.7) and total volatile fatty acids (x¯=94.3), with doses as low as 0.25%, compared with untreated hay (52.7% and 83.8 mM, respectively). However, ChNv did not decrease mold nor yeast counts (x¯=6.59 and x¯=6.16 log cfu/fresh g, respectively) and did not prevent DM losses relative to untreated hay. Overall, when using an alfalfa hay substrate in vitro, NaSP-O was able to prevent fungal spoilage to a similar extent to PRP. Thus, further studies are warranted to develop NaSP-O as a hay preservative under field conditions.
Long-Term Laryngotracheal Complications After Inhalation Injury: A Scoping Review
Authors: Zhen Emily , Misso Dylan , Rea Suzanne , Vijayasekaran Shyan , Fear Mark , Wood Fiona 
Published: April 2022

AbstractLong-term laryngotracheal complications (LTLC) after inhalation injury (II) are an under-recognized condition in patients with burns. The purpose of this study was to systematically review all available evidence on LTLC after II and identify gaps in knowledge to guide the direction of future research. A scoping review was performed to synthesize all available evidence on LTLC after II, as guided by the question, “What are the LTLC after II, in patients with or without a history of translaryngeal intubation and/or tracheostomy?”. MEDLINE, Web of Science, Ovid Embase, Cochrane Library, and Google Scholar were searched for publications on this topic. Of the 3567 citations screened, a total of 153 full-text articles were assessed for eligibility and 49 were included in the scoping review. The overall level of evidence was low, with case reports constituting 46.7% of all included human studies. The lesions were most frequently in the trachea (36.9%), followed by the glottis (34.7%) and subglottis (19.0%). LTLC occur in 4.8 to 6.5% of patients after II and these complications are under-recognized in burns patients. The risk factors for LTLC include high-grade II, elevated initial inflammatory responses, prolonged translaryngeal intubation, and a history of tracheostomy. The goal of management is to restore airway patency, preserve voice quality, and restore normal diet and swallow function. There is limited high-level evidence on LTLC, particularly with regards to long-term functional morbidity in voice and swallow. Large, prospective studies are required to address this gap in knowledge.