bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preparation of single- and double-oligonucleotide antibody conjugates and their application for protein analytics
Authors: Wiener Julius , Kokotek Daniel , Rosowski Simon , Lickert Heiko , Meier Matthias 
Published: January 2020

AbstractOligonucleotide-conjugated antibodies have gained importance for their use in protein diagnostics. The possibility to transfer the readout signal from the protein to the DNA level with an oligonucleotide-conjugated antibody increased the sensitivity of protein assays by orders of magnitude and enabled new multiplexing strategies. A bottleneck in the generation of larger oligonucleotide-conjugated antibody panels is the low conjugation yield between antibodies and oligonucleotides, as well as the lack of product purification methods. In this study, we combined a non-site-directed antibody conjugation technique using copper-free click chemistry with ion-exchange chromatography to obtain purified single and double oligonucleotide-conjugated antibodies. We optimized the click conjugation reaction of antibodies with oligonucleotides by evaluating crosslinker, reaction temperature, duration, oligonucleotide length, and secondary structure. As a result, we were able to achieve conjugation yields of 30% at a starting quantity as low as tens of nanograms of antibody, which makes the approach applicable for a wide variety of protein analytical assays. In contrast to previous non-site-directed conjugation methods, we also optimized the conjugation reaction for antibody specificity, confirmed by testing with knockout cell lines. The advantages of using single or double oligonucleotide-conjugated antibodies in regards to signal noise reduction are shown within immunofluorescence, proximity ligation assays, and single cell CITE-seq experiments.
Genome-Wide Association Study of Brain Connectivity Changes for Alzheimer’s Disease
Authors: Elsheikh Samar S. M. , Chimusa Emile R. , Mulder Nicola J. , Crimi Alessandro 
Published: January 2020

AbstractVariations in the human genome have been found to be an essential factor that affects susceptibility to Alzheimer’s disease. Genome-wide association studies (GWAS) have identified genetic loci that significantly contribute to the risk of Alzheimers. The availability of genetic data, coupled with brain imaging technologies have opened the door for further discoveries, by using data integration methodologies and new study designs. Although methods have been proposed for integrating image characteristics and genetic information for studying Alzheimers, the measurement of disease is often taken at a single time point, therefore, not allowing the disease progression to be taken into consideration. In longitudinal settings, we analyzed neuroimaging and single nucleotide polymorphism datasets obtained from the Alzheimer’s Disease Neuroimaging Initiative for three clinical stages of the disease, including healthy control, early mild cognitive impairment and Alzheimer’s disease subjects. We conducted a GWAS regressing the absolute change of global connectivity metrics on the genetic variants, and used the GWAS summary statistics to compute the gene and pathway scores. We observed significant associations between the change in structural brain connectivity defined by tractography and genes, which have previously been reported to biologically manipulate the risk and progression of certain neurodegenerative disorders, including Alzheimer’s disease.
Functional analysis of molecular and pharmacological modulators of mitochondrial fatty acid oxidation
Authors: Ma Yibao , Wang Wei , Devarakonda Teja , Zhou Huiping , Wang Xiang-Yang , Salloum Fadi N. , Spiegel Sarah , Fang Xianjun 
Published: January 2020

AbstractFatty acid oxidation (FAO) is a key bioenergetic pathway often dysregulated in diseases. The current knowledge on FAO regulators in mammalian cells is limited and sometimes controversial. Previous FAO analyses involve nonphysiological culture conditions or lack adequate quantification. We herein described a convenient and quantitative assay to monitor dynamic FAO activities of mammalian cells in physiologically relevant settings. The method enabled us to assess various molecular and pharmacological modulators of the FAO pathway in established cell lines, primary cells and mice. Surprisingly, many previously proposed FAO inhibitors such as ranolazine and trimetazidine lacked FAO-interfering activity. In comparison, etomoxir at low micromolar concentrations was sufficient to saturate its target proteins and to block cellular FAO function. Oxfenicine, on the other hand, acted as a partial inhibitor of FAO. As another class of FAO inhibitors that transcriptionally repress FAO genes, antagonists of peroxisome proliferator-activated receptors (PPARs), particularly that of PPARα, significantly decreased cellular FAO activity. Our assay also had sufficient sensitivity to monitor upregulation of FAO in response to environmental glucose depletion and other energy-demanding cues. Altogether this study provided a reliable FAO assay and a clear picture of biological properties of potential FAO modulators in the mammalian system.
Chronotype assessment via a large scale socio-demographic survey favours yearlong Standard time over Daylight Saving Time in central Europe
Authors: Sládek Martin , Kudrnáčová Röschová Michaela , Adámková Věra , Hamplová Dana , Sumová Alena 
Published: January 2020

AbstractAbandoning daylight saving time in Europe raises the topical issue of proper setting of yearlong social time, which needs mapping of various socio-demographic factors, including chronotype, in specific geographic regions. This study represents the first detailed large scale chronotyping in the Czech Republic based on data collected in the complex panel socio-demographic survey in households (total 8760 respondents) and the socio-physiological survey, in which chronotyped participants also provided blood samples (n = 1107). Chronotype assessment based on sleep phase (MCTQ questions and/or time-use diary) correlated with a self-assessed interval of best alertness. The mean chronotype of the Czech population defined as mid sleep phase (MSFsc) was 3.13 ± 0.02 h. Chronotype exhibited significant east-to-westward, north-to-southward, and settlement size-dependent gradients and was associated with age, sex, partnership, and time spent outdoors as previously demonstrated. Moreover, for subjects younger than 40 years, childcare was highly associated with earlier chronotype, while dog care was associated with later chronotype. Body mass index correlated with later chronotype in women whose extreme chronotype was also associated with lower plasma levels of protective HDL cholesterol. Based on the chronotype prevalence the results favour yearlong Standard Time as the best choice for this geographic region.
RETRACTED ARTICLE: A Complete Formula of Ocean Surface Absolute Geostrophic Current
Authors: Chu Peter C. 
Published: January 2020

AbstractAbsolute geostrophic current at the ocean surface (S) contains three components: (1) absolute geostrophic current at the geoid undulation (N), (2) geostrophic shear (betweenSandN) due to horizontal gradient of dynamic ocean topography, and (3) geostrophic shear (betweenSandN) due to horizontal gradient of density. However, only the second component is used to represent the surface absolute geostrophic current in physical oceanography and satellite geodesy. Four public datasets are used to calculate each component. Evident difference between the surface absolute geostrophic current and the second component (i.e., geostrophic shear due to horizontal gradient of dynamic ocean topography) was found by the statistical characteristics with the relative root mean square difference of 0.605. It shows that the common practice in physical oceanography and satellite geodesy is not correct. The horizontal gradient of dynamic ocean topography alone cannot be claimed as the surface absolute geostrophic current.
A Novel Loss-of-Function Variant in the Chloride Ion Channel Gene Clcn2 Associates with Atrial Fibrillation
Authors: Hansen Thea Hyttel , Yan Yannan , Ahlberg Gustav , Vad Oliver Bundgaard , Refsgaard Lena , dos Santos Joana Larupa , Mutsaers Nancy , Svendsen Jesper Hastrup , Olesen Morten Salling , Bentzen Bo Hjorth , Schmitt Nicole 
Published: January 2020

AbstractAtrial Fibrillation (AF) is the most common cardiac arrhythmia. Its pathogenesis is complex and poorly understood. Whole exome sequencing of Danish families with AF revealed a novel four nucleotide deletion c.1041_1044del in CLCN2 shared by affected individuals. We aimed to investigate the role of genetic variation of CLCN2 encoding the inwardly rectifying chloride channel ClC-2 as a risk factor for the development of familiar AF. The effect of the CLCN2 variant was evaluated by electrophysiological recordings on transiently transfected cells. We used quantitative PCR to assess CLCN2 mRNA expression levels in human atrial and ventricular tissue samples. The nucleotide deletion CLCN2 c.1041_1044del results in a frame-shift and premature stop codon. The truncated ClC-2 p.V347fs channel does not conduct current. Co-expression with wild-type ClC-2, imitating the heterozygote state of the patients, resulted in a 50% reduction in macroscopic current, suggesting an inability of truncated ClC-2 protein to form channel complexes with wild type channel subunits. Quantitative PCR experiments using human heart tissue from healthy donors demonstrated that CLCN2 is expressed across all four heart chambers. Our genetic and functional data points to a possible link between loss of ClC-2 function and an increased risk of developing AF.
Heat stress modulates differential response in skin fibroblast cells of native cattle (Bos indicus) and riverine buffaloes (Bubalus bubalis)
Authors: Shandilya Umesh K. , Sharma Ankita , Sodhi Monika , Mukesh Manishi 
Published: January 2020

Abstract
Heat stress in hot climates is a major cause that negatively affects dairy animals, leading to substantial economic loss. The present study was aimed to analyze the effect of heat stress on cellular and molecular levels in dermal fibroblast of cattle and buffaloes. Primary fibroblast culture was established using ear pinna tissue samples of cattle (Bos indicus) and riverine buffaloes (Bubalus Bubalis). The cells were exposed to thermal stress at 42°C for 1 h and subsequently allowed to recover and harvest at 37°C at different time points (0, 2, 4, 8, 16, and 24 h) along with control samples. Different cellular parameters viz., apoptosis, proliferation, mitochondrial membrane potential (ΔΨm), oxidative stress, along with expression pattern of heat responsive genes and miRNAs were determined. Cell viability and proliferation rate of heat-stressed fibroblasts decreased significantly (P &lt; 0.05) albeit to a different extent in both species. The cell cytotoxicity, apoptosis, production of reactive oxygen species, and ΔΨm increased more significantly (P &lt; 0.01) in heat stressed fibroblasts of buffalo than cattle. The pattern of heat shock proteins, inflammation/immune genes, and heat responsive miRNA showed differences in induction of their expression level in buffalo and native cattle fibroblasts. Conclusively, finding indicates that heat stress induces more profound impact on buffalo fibroblasts than native cattle fibroblasts. The differential response of cellular parameters, HSP genes, and miRNA expression could be due to better adaptive capacity of skin fibroblast of Bos indicus cattle in comparison with riverine buffaloes.
The effects of the M2a macrophage-induced axonal regeneration of neurons by arginase 1
Authors: Zhang Jieyuan , Li Yue , Duan Zhaoxia , Kang Jianyi , Chen Kuijun , Li Guanhua , Weng Changmei , Zhang Dongdong , Zhang Lu , Wang Jianmin , Li Bingcang 
Published: January 2020

Abstract
Background: Spinal cord injury (SCI) is a challenge worldwide, but there are no effective treatments or therapeutic methods in the clinic. Recent studies have shown that type I arginase (Arginase1, Arg1) is closely associated with the treatment of SCI. The classical treatment for SCI involves filling the local area of SCI with activated M2a macrophages to allow the repair and regeneration of some synapses, but the specific mechanism of action of Arg1 is not clear.
Method: In the present study, we first induced the polarization of RAW264.7 macrophages to M2a-type cells using IL-4 and constructed an Arg1 knockout cell line through the use of shRNA; we used these cells to treat a rat model of SCI. Finally, the present study explored the mechanism and pathway by which Arginase 1 regulates spinal repair by immunoblotting and immunohistochemistry.
Result: Suspended M2a (Arg1-/+) macrophages were transplanted into the injury site in a rat model of contusion SCI. Compared with the model group and the shArg1 group, the shScramble (shSc) group exhibited higher Basso, Beattie, Bresnahan motor function scores, more compact structures and more Nissl bodies. Immunohistochemical results showed that the shSc group expressed higher levels of NeuN (a neuronal marker) and tau (an axonal marker), as well as the up-regulation of Cdc42, N-WASP, Arp2/3 and tau, as determined by Western blot.
Conclusion: The study found that the polarization of M2a macrophages promoted the expression of Arginase 1, which restored axonal regeneration, promoted axonal regeneration, and promoted the structural and functional recovery of the contused spinal cord.
Pediatric Dysphagia: Survey Results Describing Speech-Language Pathologists' Education and Experience
Authors: Wilson Jennifer J. , Simmons Amanda K. , H. McCarthy Jillian 
Published: January 2020

Purpose
Evaluation and treatment of pediatric dysphagia, swallowing difficulties occurring during childhood, is in the speech-language pathologists' (SLPs) scope of practice; however, little is known regarding the education SLPs receive during their graduate work and afterwards to effectively assess, treat, and manage this diagnosis.

Method
An 11-question survey was developed to examine the experience and opinions of SLPs related to the type and extent of pediatric dysphagia education and training they have and/or should have received during their graduate education. The survey was disseminated to SLPs across the United States via social media and e-mail Listservs.

Results
Survey results from 134 participants across the country, with varying clinical backgrounds, indicated a lack of pediatric dysphagia education during graduate school. SLPs reported overcoming these insufficiencies through gaining work experience and pursuing continuing education units on pediatric dysphagia. SLPs overwhelmingly (> 95% of respondents) recommended a full course or unit focusing on pediatric dysphagia for master's students in speech-language pathology. Survey results found a statistically significant increase in the likelihood of completion of a pediatric dysphagia unit or course for students graduating in the last 10 years; however, this positive trajectory shows a modest increase in the availability of coursework to prepare pediatric SLPs to evaluate and treat the growing pediatric dysphagia population.

Conclusions
Some positive changes in SLP education can be inferred from these results; however, there is still additional work to be done to equip pediatric SLPs to provide adequate care for a growing population with pediatric dysphagia.
Adults Who Stutter and Their Motivation for Attending Stuttering Support Groups: A Pilot Study
Authors: Medina Angela M. , Almeida Naiceli , Amarante Kayleen , Martinez Natalie , Prezzemolo Michele 
Published: January 2020

Purpose
While the benefits of participating in stuttering support groups are well known, the factors that motivate adults who stutter (AWS) to continue attending these meetings are not documented. The purpose of this exploratory study is to investigate the narratives of AWS and identify their individual motivations for regularly attending stuttering support groups.

Method
Seven AWS, ages 23–54 years, who attended more than one stuttering support group meeting participated in a semistructured interview about their stuttering and their experiences participating in a stuttering support group. Thematic analysis procedures were followed to investigate descriptions of motivating factors in each participant's narrative.

Result
Four major themes emerged from the data including “Mutual Understanding and Common Ground,” “Support Group Format,” “Positive Changes,” and “Give and Take of the Support Group.” The support group served as a place to gain new perspectives by watching others who stutter more severely communicate while also creating a sense of not being “alone.” Opportunities to speak and/or stutter freely as well as the role chapter leaders take in facilitating conversation were motivating factors in terms of the support group format. Positive changes in emotional well-being and socialization were reported. Participants also stated that they attend support groups because the group provides them with an opportunity to help others and learn from others.

Conclusion
This exploratory study uncovered particular aspects of support groups, including group members and the structure of meetings, that motivate AWS to attend. Findings support the literature in that participants reported benefiting from participating in support groups.
Machines de vie, machines de mort : la famille à l’épreuve des soins machinisés
Authors: Jean-Dit-Pannel Romuald , Thomas François 
Published: January 2020

Des machines médicales tiennent en vie des sujets en soins intensifs, en hémodialyse. Le soin somatique est à la fois médical, technique, machinique/machinisé et robotique/robotisé. Ces machines de vie et de mort sont vécues comme des corps étranges et étrangers, par le sujet lui-même, par son entourage, notamment familial.
Avec le cas d’une femme hémodialysée qui a perdu un fils en soins intensifs, nous illustrerons comment une famille tout entière peut se trouver dans l’engrenage de soins machinisés, machiniques, et le rester in(dé)finiment.
Radio observatories and instrumentation used in space weather science and operations
Authors: Carley Eoin P. , Baldovin Carla , Benthem Pieter , Bisi Mario M. , Fallows Richard A. , Gallagher Peter T. , Olberg Michael , Rothkaehl Hanna , Vermeulen Rene , Vilmer Nicole , Barnes David ,   the LOFAR4SW Consortium
Published: January 2020

The low frequency array (LOFAR) is a phased array interferometer currently consisting of 13 international stations across Europe and 38 stations surrounding a central hub in the Netherlands. The instrument operates in the frequency range of ~10–240 MHz and is used for a variety of astrophysical science cases. While it is not heliophysics or space weather dedicated, a new project entitled “LOFAR for Space Weather” (LOFAR4SW) aims at designing a system upgrade to allow the entire array to observe the Sun, heliosphere, Earth’s ionosphere, and Jupiter throughout its observing window. This will allow the instrument to operate as a space weather observing platform, facilitating both space weather science and operations. Part of this design study aims to survey the existing space weather infrastructure operating at radio frequencies and show how LOFAR4SW can advance the current state-of-the-art in this field. In this paper, we survey radio instrumentation and facilities that currently operate in space weather science and/or operations, including instruments involved in solar, heliospheric, and ionospheric studies. We furthermore include an overview of the major space weather service providers in operation today and the current state-of-the-art in the radio data they use and provide routinely. The aim is to compare LOFAR4SW to the existing radio research infrastructure in space weather and show how it may advance both space weather science and operations in the radio domain in the near future.
Robotic perineal radical prostatectomy in a patient with a pre-existing three piece inflatable penile prosthesis
Authors: Yenice Mustafa Gurkan , Yigitbasi Ismail , Sam Emre , Simsek Abdulmuttalip , Tugcu Volkan 
Published: January 2020

AbstractRadical prostatectomy (RP) is the primary and standard treatment for localized prostate cancer. As in many surgical procedures, RP can now be accomplished through minimally invasive methods. RP in a patient with a pre-existing 3-piece inflatable penile prosthesis (IPP) is an exceptional condition and involves coping with many difficulties. In this case report, we aimed to present a patient with pre-existing 3-piece IPP for whom we successfully performed robotic perineal RP (r-PRP).
Role of CTA in Women with Abdominal Scars Undergoing DIEP Breast Reconstruction: Review of 1,187 Flaps
Authors: Daly Lauren T. , Doval Andres F. , Lin Samuel J. , Tobias Adam , Lee Bernard T. , Dowlatshahi A. Samandar 
Published: January 2020

Abstract
Background This study examines the effect of prior abdominal surgery on flap, donor-site, and overall complications in women undergoing deep inferior epigastric artery perforator (DIEP) flap breast reconstruction and assesses whether preoperative computed tomography angiography (CTA) affects outcomes.
Methods All DIEP flaps performed at our institution between 2004 and 2015 were identified retrospectively. Patients were stratified based on a history of prior abdominal surgery and whether or not they underwent a preoperative CTA. A subgroup analysis was performed to compare operative times and incidence of complications using adjusted odds ratios (ORs).
Results Over a 12-year period, 425 patients (640 flaps) had prior abdominal surgery, and 393 patients (547 flaps) had no prior abdominal surgery. Of the patients with previous abdominal surgery, 67 (15.7%) underwent preoperative CTA and 333 (78.4%) did not. Patients with prior abdominal surgery were more likely to have donor-site wound complications (OR: 1.82, 95% confidence interval [CI]: 1.15–2.87, p = 0.01), fat necrosis ≥2cm of the transferred flap (OR: 1.39, 95% CI: 1.0–1.94, p = 0.05), and were more likely to have bilateral DIEP flap reconstruction (OR: 1.61, 95% CI: 1.22–2.12, p < 0.001). Preoperative CTA did not reduce the risk of complications and did not affect operative times.
Conclusion DIEP flap reconstruction can be safely performed in women with prior abdominal surgery. However, these patients should be counseled that they are at an increased risk for donor-site wound breakdown and fat necrosis of the reconstructed breast. Preoperative CTA does not reduce complication rate, overall operative time, or time needed to dissect perforators in women with abdominal scars.
Quantification in Musculoskeletal Imaging Using Computational Analysis and Machine Learning: Segmentation and Radiomics
Authors: Bach Cuadra Meritxell , Favre Julien , Omoumi Patrick 
Published: January 2020

AbstractAlthough still limited in clinical practice, quantitative analysis is expected to increase the value of musculoskeletal (MSK) imaging. Segmentation aims at isolating the tissues and/or regions of interest in the image and is crucial to the extraction of quantitative features such as size, signal intensity, or image texture. These features may serve to support the diagnosis and monitoring of disease. Radiomics refers to the process of extracting large amounts of features from radiologic images and combining them with clinical, biological, genetic, or any other type of complementary data to build diagnostic, prognostic, or predictive models. The advent of machine learning offers promising prospects for automatic segmentation and integration of large amounts of data. We present commonly used segmentation methods and describe the radiomics pipeline, highlighting the challenges to overcome for adoption in clinical practice. We provide some examples of applications from the MSK literature.