bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clickable report tags for identification of modified peptides by mass spectrometry
Authors: Makarov Dmytro , Telek András , Becker Tobias , von Wrisberg Marie‐Kristin , Schneider Sabine , Kielkowski Pavel 
Published: January 2022

AbstractThe identification and quantification of modified peptides are critical for the functional characterization of post‐translational protein modifications (PTMs) to elucidate their biological function. Nowadays, quantitative mass spectrometry coupled with various bioinformatic pipelines has been successfully used for the determination of a wide range of PTMs. However, direct characterization of low abundant protein PTMs in bottom‐up proteomic workflow remains challenging. Here, we present the synthesis and evaluation of tandem mass spectrometry tags (TMT) which are introduced via click‐chemistry into peptides bearing alkyne handles. The fragmentation properties of the two mass tags were validated and used for screening in a model system and analysis of AMPylated proteins. The presented tags provide a valuable tool for diagnostic peak generation to increase confidence in the identification of modified peptides and potentially for direct peptide‐PTM quantification from various experimental conditions.
Indian spices: past, present and future challenges as the engine for bio‐enhancement of drugs: impact of COVID‐19
Authors: Gidwani Bina , Bhattacharya Ruchi , Shukla Shiv Shankar , Pandey Ravindra Kumar 
Published: January 2022

AbstractSpices are natural plant products enriched with the history of being used as herbal medicine for prevention of diseases. India is also known as the ‘Land of Spices’. Out of 109 spices recognized by the International Organization for Standardization (ISO) more than 52–60 spice crops are grown in India. The major spices exported by India are turmeric, cumin, coriander, fenugreek, peppers, etc. The Indian spices are divided into three era viz. early period, middle age and early modern period. Spices are used in beverages, liquors, and pharmaceutical, cosmetic and perfumery products. The major issue with spices is their handling and storage. This review article mainly focuses on two aspects: at the outset the handling and storage of the spices is an essential factor as spices are available in different forms like raw, processed, fresh, whole dried, or pre‐ground dried. Therefore, the need of processing, packaging, storage and handling of the spices is important as the deterioration of spices can lead to the loss of therapeutic activity. Furthermore, many herbal constituents have the capability to enhance the bioavailability of drugs. Therefore, an attempt has been made to throw a light on the bioenhancer activity and therapeutic activity along with their mechanism of action of some Indian spices which are regularly used for cooking purpose on a daily basis to enhance the taste of food. The spices suggested by ministry of AYUSH which is relevant to its medicinal and biological property in treatment and prevention from COVID‐19 are discussed. © 2022 Society of Chemical Industry.
Preparation and characterization of konjac glucomannan (KGM) and deacetylated KGM (Da‐KGM) obtained by sonication
Authors: Ye Shuxin , Zhu Jingsong , Shah Bakht Ramin , Abel Wend‐Soo Zongo , Li Jing , Zhan Fuchao , Li Bin 
Published: January 2022

AbstractBACKGROUNDKonjac glucomannan (KGM) has been widely applied in the food industry as a thickening and gelation agent because of its unique colloidal properties of viscosity enhancement and gelling ability. The current study aimed to prepare and characterize KGM and deacetylated KGM (Da‐KGM) samples obtained by sonication in neutral and alkali ethanol–water solutions.RESULTSThe results showed that the deacetylation degree (DD) of Da‐KGM increased exponentially with alkali concentration. Fourier transform infrared spectrometry further confirmed the deacetylation reaction through the dramatic decrease in the acetyl group band at 1740 cm−1. Besides, the high similarity among the tested groups in terms of X‐ray diffraction (XRD) spectra implied a similar crystalline structure, while differential scanning calorimetry (DSC) curves revealed that the water binding capacity and decomposition temperature of KGM changed slightly with alkali and sonication treatment. The rheological profiles indicated that apparent viscosity (η0) of sonicated KGM samples was unchanged except for the T60 group (60 min sonication treatment). Particularly, ultrasonic treatment under high alkaline conditions (0.10 mol L−1 NaOH) was noted to promote the deacetylation reaction, and the obtained samples showed decreased apparent viscosity and weakened the gelation process in aqueous solution. Partial correction analysis indicated that alkali rather than ultrasonic treatment resulted in the change of DD and η0 in Da‐KGM. Moreover, sonication contributed to off‐white color by reducing the browning caused by alkali in Da‐KGM products.CONCLUSIONUltrasound‐mediated heterogeneous deacetylation reaction is a feasible way to prepare Da‐KGM samples with lightened browning and controllable DD. © 2022 Society of Chemical Industry.
Black bear spatial responses to the Wallow Wildfire in Arizona
Authors: Crabb Michelle L. , Clement Matthew J. , Jones Andrew S. , Bristow Kirby D. , Harding Larisa E. 
Published: January 2022

AbstractThe Wallow Fire, the largest wildfire in Arizona history, encompassed 2,170 km2and provided a rare opportunity to examine habitat selection and home ranges of American black bears (Ursus americanus) before and after a wildfire. We had fitted global positioning system (GPS) collars on 47 bears from 2005 to April 2011, and 10 of these were still collared when the fire started in May 2011. We captured and collared an additional 7 black bears within the fire perimeter post‐fire (Jul–Sep 2011 and Jun 2012). To evaluate how black bears were affected by the fire, we fit a step selection function using a conditional mixed effects Poisson regression model to estimate the relative strength of black bear habitat selection in response to burn severity. Additionally, we estimated home range sizes using an autocorrelated kernel density estimator by means of a continuous‐time movement model. We then used a generalized linear model with a negative binomial error distribution and mixed effects to estimate the effect of the burn severity on black bear home range size, while controlling for sex and drought. In spring and summer in years prior to the fire, bears selected areas that later burned in the fire. After the fire, bears used all burn severities, but their selection for high‐severity burns decreased significantly in summer 2011 and fall 2012. Home range sizes were 3.06 times larger pre‐fire than post‐fire. Our study demonstrates that black bears continued to use all burn severities after a major wildfire, and that post‐fire conditions did not result in expanded black bear home ranges.
Integrating distance sampling survey data with population indices to separate trends in abundance and temporary immigration
Authors: Schmidt Joshua H. , Wilson Tammy L. , Thompson William L. , Mangipane Buck A. 
Published: January 2022

AbstractManagers rely on accurate estimators of wildlife abundance and trends for management decisions. Despite the focus of contemporary wildlife science on developing methods to improve inference from wildlife surveys, legacy datasets often rely on index counts that lack information about the detection process. Data integration can be a useful tool for combining index counts with data collected under more rigorous designs (i.e., designs that account for the detection process), but care is required when datasets represent different population processes or are mismatched in space and time. This can be particularly problematic in cases where animals aggregate in response to a spatially or temporally limited resource because individuals may temporarily immigrate from outside the study area and be included in the abundance index. Abundance indices based on brown bear (Ursus arctos) feeding aggregations within coastal meadows in early summer in Lake Clark National Park and Preserve, Alaska, USA, are one such example. These indices reflect the target population (brown bears residing within the park) and temporary immigrants (i.e., bears drawn from outside the park boundary). To properly account for the effects of temporary immigration, we integrated the index data with abundance data collected via park‐wide distance sampling surveys, the latter of which properly addressed the detection process. By assuming that the distance data provide inference on abundance and the index counts represent some combination of abundance and temporary immigration processes, we were able to decompose the relative contribution of each to overall trend. We estimated that the density of brown bears within our study area was 38–54 adults/1,000 km2 during 2003–2019 and that abundance increased at a rate of approximately 1.4%/year. The contribution of temporary immigrants to overall trend in the index was low, so we created 3 hypothetical scenarios to more fully demonstrate how the integrated approach could be useful in situations where the composite trend in meadow counts may obscure trends in abundance (e.g., opposing trends in abundance and temporary immigration). Our work represents a conceptual advance supporting the integration of legacy index data with more rigorous data streams and is broadly applicable in cases where trends in index values may represent a mixture of population processes.
Recurrent Laryngeal Nerve Paralysis Following Thyroidectomy: Analysis of Factors Affecting Nerve Recovery
Authors: Mohammad Ramla , Huh Gene , Cha Wonjae , Jeong Woo‐Jin 
Published: January 2022

ObjectivesParalysis of the recurrent laryngeal nerves (RLNs), albeit decreased over the years, leaves the surgeon helpless as there is not much that can be done once it occurs. Nimodipine has been suggested as a remedy that could accelerate the recovery of the nerve. Our study aimed to examine the factors that affect the recovery rate (RR) and time to recovery (TTR) of post‐thyroidectomy RLN paralysis, with an emphasis on the use of nimodipine.MethodsA total of 197 patients who had undergone thyroid and parathyroid surgeries were retrospectively reviewed from October 2016 to August 2019. Patients who had RLN paralysis following surgery were assessed. The medical records were retrospectively analyzed to look for possible factors that may influence RLN recovery.ResultsA total of 289 nerves were at risk. Temporary RLN paralysis rate was 7.9% while 1.7% was permanent. Age (odds ratio [OR] = 4.8) and intra‐operative extra‐thyroid extension (OR = 9.0) were independent risk factors for RLN paralysis. The rate of recovery was 82.1%. Loss of signal (LOS; P = .066) was a factor trending for an impact on RR but not nimodipine (P > .05). The mean TTR was 32 days. LOS, nimodipine, and steroid use, among others, were factors trending for an impact on the TTR.ConclusionAlthough not reaching statistical significance, nimodipine and steroids might influence TTR but not the RR. Larger studies are warranted to address the effect of nimodipine on the outcome of RLN paralysis.Level of Evidence4 Laryngoscope, 132:1692–1696, 2022
Detection of soil pipe network by geophysical approach: Electromagnetic induction (EMI) and electrical resistivity tomography (ERT)
Authors: Bernatek‐Jakiel Anita , Kondracka Marta 
Published: January 2022

AbstractStudying soil pipes is a methodological challenge that needs improvement in detection methods in order to better recognize the role of piping erosion in land degradation and hillslope hydrology. This study explores electromagnetic induction (EMI) and electrical resistivity tomography (ERT) in order to identify soil pipes. The study was conducted in a mountainous area (the Bieszczady Mountains, SE Poland) under a temperate climate, where pipes develop in silty‐clayey soils. In the plot area, eight profiles were measured by the conductivity meter at different depths and then interpolated to present apparent electrical conductivity (ECa). Also, six ERT profiles were carried out using the Wenner‐Schlumberger electrode configuration. The ECa values measured by EMI are not very diversified, suggesting its lower sensitivity to changes in the ECa, whereas the ECa values measured by ERT are characterized by greater fluctuation, that is, better detection possibilities. ERT has revealed soil pipes as zones of higher electrical resistivity (ER >268 Ωm) than their surroundings (characterized below pipes by ER <105 Ωm) underlying the air filling of pipes (ER >427 Ωm), whereas EMI has revealed its higher sensitivity to water content. The EMI results have shown the lowering of the water table in the lower part of the slope, perhaps because of the drainage by a complex pipe network. EMI allows quick measurements of ECa providing information on water content, and thus indirectly soil pipes, but, it cannot delineate individual pipes. Only the integration of geophysical methods supported by field recognition provides an effective method to detect soil pipes.
Case series of photic maculopathy associated with exposure to a plasma flash induced by a femtosecond laser
Authors: Jiang Fagang , Shi Yao , Wang Zhi , Yang Xiaobo 
Published: January 2022

AbstractBackground and ObjectivesPhotic maculopathy resulting from laser‐induced plasma flash has been rarely reported, and the corresponding mechanism of the injury is still unclear. We present a case series of three patients with bilateral macular injuries produced by exposure to the plasma radiation from femtosecond laser tightly focusing.Study Design/Materials and MethodsFunduscopic findings were accompanied mainly by optical coherence tomography (OCT) investigation of the macula during the follow‐up period.ResultsAll patients shared similar clinical symptoms soon after the initial injury, including reduced visual acuity and central scotomas. It was acutely characterized by foveolar yellowish faceted lesions upon fundus examination. The main OCT finding in the acute stage was a hyper‐reflective area involving all foveolar retinal layers without retinal edema. Repeat OCT evaluation during the latter stages revealed that the retinal changes were reversible, but delineated mild pathology at the outer foveal retina. This retinal structural recovery was accompanied by improvements in visual acuity and central scotomas as well.ConclusionsProlonged viewing of a plasma flash induced by a focused femtosecond laser without eye protection may produce persistent damage to the retina. We believe that a photochemical process similar to the mechanism of a solar burn or welder's maculopathy may cause retinal damage in this case series.
Colloid Syringeless Electrospinning toward Nonwoven Nanofiber Web Containing a Massive Amount of Inorganic Fillers
Authors: Lee Jaeyu , Lee Kyung Jin 
Published: January 2022

AbstractColloidal electrospinning is identified as a powerful tool for the fabrication of nonwoven nanofiber webs with increased functionality by the introduction of functional fillers into the webs. However, the use of this method is still limited due to minimal material diversity, low concentration of fillers, difficulty in mass production, and process difficulties. In this paper, syringeless electrospinning is suggested as an excellent method for colloidal electrospinning. Since the polymeric solution is supplied from the container through rotating drums, this method is relatively free from the precipitation of fillers present in the polymeric solution. Syringeless electrospinning provides a higher production rate than needle‐based electrospinning with simple process control. The syringeless technique makes it possible to expand the scope of the method to various polymers and inorganic fillers with sufficiently high filler concentrations. Herein, nonwoven nanofiber webs with a diverse combination of polymers (polyacrylonitrile (PAN), thermoplastic polyurethane (TPU), and polyvinylpyrrolidone (PVP)) and fillers (silica, titania, zirconia, activated carbons, and metal‐organic framework (MOF) crystals) are presented. Nonwoven nanofiber webs comprising PAN and UiO‐66‐NH2 MOF crystal are prepared for detoxification of a nerve agent simulant, diisopropyl fluorophosphate (DFP), as a representative example of applications.
Periodicity on isolated time scales
Authors: Bohner Martin , Mesquita Jaqueline , Streipert Sabrina 
Published: January 2022

AbstractIn this work, we formulate the definition of periodicity for functions defined on isolated time scales. The introduced definition is consistent with the known formulations in the discrete and quantum calculus settings. Using the definition of periodicity, we discuss the existence and uniqueness of periodic solutions to a family of linear dynamic equations on isolated time scales. Examples in quantum calculus and for mixed isolated time scales are presented.
Air Pollution and the Risk of Parkinson's Disease: A Review
Authors: Murata Hiromi , Barnhill Lisa M. , Bronstein Jeff M. 
Published: January 2022

ABSTRACTParkinson's disease, as well as other neurodegenerative disorders, are primarily characterized by pathological accumulation of proteins, inflammation, and neuron loss. Although there are some known genetic risk factors, most cases cannot be explained by genetics alone. Therefore, it is important to determine the environmental factors that confer risk and the mechanisms by which they act. Recent epidemiological studies have found that exposure to air pollution is associated with an increased risk for development of Parkinson's disease, although not all results are uniform. The variability between these studies is likely due to differences in what components of air pollution are measured, timing and methods used to determine exposures, and correction for other variables. There are several potential mechanisms by which air pollution could act to increase the risk for development of Parkinson's disease, including direct neuronal toxicity, induction of systemic inflammation leading to central nervous system inflammation, and alterations in gut physiology and the microbiome. Taken together, air pollution is an emerging risk factor in the development of Parkinson's disease. A number of potential mechanisms have been implicated by which it promotes neuropathology providing biological plausibility, and these mechanisms are likely relevant to the development of other neurodegenerative disorders such as Alzheimer's disease. This field is in its early stages, but a better understanding of how environmental exposures influence the pathogenesis of neurodegeneration is essential for reducing the incidence of disease and finding disease‐modifying therapies. © 2022 International Parkinson and Movement Disorder Society
Genetic of preimplantation diagnosis of dysmorphic facial features and intellectual developmental disorder (CHDFIDD) without congenital heart defects
Authors: Cui Xiangrong , Wu Xueqing , Wang Hongwei , Zhang Sanyuan , Wang Wei , Jing Xuan 
Published: January 2022

AbstractBackgroundCyclin‐dependent kinase 13 plays a critical role in the regulation of gene transcription. Recent evidence suggests that heterozygous variants in CDK13 are associated with a syndromic form of mental deficiency and developmental delay, which is inherited in an autosomal dominant manner.MethodsA mentally retarded mother (33‐year‐old) and son (10‐year‐old boy) in our hospital with CDK13 variant (c.2149 (exon 4) G>A. p.Gly717Arg) were detected by whole‐exome sequencing (WES). All published CDK13 variant syndrome cases as of November 11, 2021, were searched, and their clinical information was recorded and summarized.ResultsWe studied two patients in a Chinese family with a heterozygous constitutional CDK13 variant (c.2149 (exon 4) G>A. p.Gly717Arg), exhibiting the classical characteristics of dysmorphic facial features and intellectual developmental disorder (CHDFIDD, OMIM # 617360), without congenital heart defects. This is the first reported case of an adult patient with a CDK13 variant that gave birth to the next generation with the same variant. Preimplantation genetic testing for monogenic disease (PGT‐M) was performed for the proband and her husband with full informed consent and successfully blocked the inheritance of the disease.ConclusionOur study is of great significance for molecular diagnosis and genetic counseling of patients with CDHFIDD and extends the variant spectrum of CDK13.
Phenotypic heterogeneity in patients with NEFL‐related Charcot–Marie–Tooth disease
Authors: Kim Hye Jin , Kim Sang Beom , Kim Hyun Su , Kwon Hye Mi , Park Jae Hong , Lee Ah Jin , Lim Si On , Nam Soo Hyun , Hong Young Bin , Chung Ki Wha , Choi Byung‐Ok 
Published: January 2022

AbstractCharcot–Marie–Tooth disease (CMT) is the most common hereditary peripheral neuropathy. Mutations in the neurofilament light polypeptide (NEFL) gene produce diverse clinical phenotypes, including demyelinating (CMT1F), axonal (CMT2E), and intermediate (CMTDIG) neuropathies. From 2005 to 2020, 1,143 Korean CMT families underwent gene sequencing, and we investigated the clinical, genetic, and neuroimaging spectra of NEFL‐related CMT patients. Ten NEFL mutations in 17 families (1.49%) were identified, of which three (p.L312P, p.Y443N, and p.K467N) were novel. Eight de novo cases were identified at a rate of 0.47 based on a cosegregation analysis. The age of onset was ≤3 years in five cases (13.5%). The patients revealed additional features including delayed walking, ataxia, dysphagia, dysarthria, dementia, ptosis, waddling gait, tremor, hearing loss, and abnormal visual evoked potential. Signs of ataxia were found in 26 patients (70.3%). In leg MRI analyses, various degrees of intramuscular fat infiltration were found. All compartments were evenly affected in CMT1F patients. The anterior and anterolateral compartments were affected in CMT2E, and the posterior compartment was affected in CMTDIG. Thus, NEFL‐related CMT patients showed phenotypic heterogeneities. This study's clinical, genetic, and neuroimaging results could be helpful in the evaluation of novel NEFL variants and differential diagnosis against other CMT subtypes.
Analysis of risk factors for complications of perforator propeller flaps used for soft tissue reconstruction after malignant tumor resection: A systematic review and meta‐analysis
Authors: Yue Shuai , Ju Mengran , Su Zhe 
Published: January 2022

AbstractBackgroundPerforator propeller flaps (PPFs) have been widely used due to their numerous advantages; however, they were also associated with various complications. Herein, we analyzed the risk factors for complications of PPFs used for soft tissue reconstruction after malignant tumor resection.MethodsWe searched databases for articles on soft tissue reconstruction using PPFs after malignant tumor resection published between January 1991 and April 2021. Studies were selected according to the preferred reporting items for systematic reviews and meta‐analyses (PRISMA) statement. Fixed effects models and relative risks were used for data analysis. Funnel plots and Begg's test were used to evaluate publication bias.ResultsTwenty‐six articles met the inclusion criteria. Complications were found in 24.7% of all patients. The four significant risk factors were age equal or older than 60 years (pooled relative risk, 1.83; p = .04), smoking (pooled relative risk, 2.32; p = .03), diabetes (pooled relative risk, 2.59; p = .01) and radiotherapy (pooled relative risk, 2.09; p = .01). Hypertension, defects located in the extremities, flap size equal or greater than 100 cm2, and pedicle rotation equal or greater than 120 degrees were not significant risk factors for complications. No publication bias was found in the included articles.ConclusionAge equal or older than 60 years, smoking, diabetes and radiotherapy are four risk factors for complications when PPFs are used to reconstruct soft tissue defects resulting from malignant tumor resection.