bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling myosin with interacting linkages
Authors: Omabegho Tosan 
Published: April 2021

AbstractIn this study, I describe a model in which mechanical linkages dynamically interact in a stepwise and reversible manner, and use it to model the chemical cycle and lever arm action of the biomolecular motor myosin. Myosin is emulated using a series of multivalent chemical reactions between a linkage enzyme and four reactants: a cleaveable fuel, two cleavage products, and ligand. Geometric coupling between the fuel and ligand binding sites—an analog for negative allosteric coupling—allows reaction sequences similar to nucleotide exchange to take place that in turn drive the “strokes” of the machine’s lever arm. Cyclic chemical behavior is demonstrated by stochastic simulation, and mechanical activity by a series of logical arguments. I show how a reciprocal and nonreciprocal conformational cycle emerge from the allosteric rules designed to achieve chemical cycling, and how the non-reciprocal cycle can break directional symmetry along a track like structure. A dimeric construct is used to demonstrate how directed motion can be designed by inhibition of the reciprocal cycle and reinforcement of the non-reciprocal cycle, through allosteric feedback between the units of the dimer. By showing how the chemomechanical cycle of a biomolecular motor can be recreated with simple geometric and chemical principles, this work may help advance the rational design of allosteric mechanisms, and the development of synthetic molecular motors.
Unmethylated Regions Encompass The Functional Space Within The Maize Genome
Authors: Ricci William 
Published: April 2021

AbstractDelineating the functional space within genomes has been a long-standing goal shared among geneticists, molecular biologists, and genome scientists. The genome of Zea mays (maize) has served as a model for locating functional elements within the gene-distal intergenic space. A recent development has been the discovery and use of accessible chromatin as a proxy for functional regulatory elements. However, the idea has recently arisen that DNA methylation data could supplement the use of accessible chromatin data for homing in on regulatory regions. Here, I test the robustness of using DNA methylation as a proxy for functional space. I find that CHG methylation can be non-arbitrarily partitioned into hypo-methylated and hyper-methylated regions. Hypo-methylated CHG regions are stable across development and contain nearly all accessible chromatin. Note: changes that will be made in version 2: expand introduction; expand discussion; add additional analyses; expand methods; link to github scripts.
The genetic basis of structural colour variation in mimeticHeliconiusbutterflies
Authors: Brien Melanie N. , Romero Juan Enciso , Lloyd Victoria J. , Curran Emma V. , Parnell Andrew J. , Morochz Carlos , Salazar Patricio A. , Rastas Pasi , Zinn Thomas , Nadeau Nicola J. 
Published: April 2021

AbstractStructural colours, produced by the reflection of light from ultrastructures, have evolved multiple times in butterflies. Unlike pigmentary colours and patterns, little is known about the genetic basis of these colours. Reflective structures on wing-scale ridges are responsible for iridescent structural colour in many butterflies, including the Müllerian mimicsHeliconius eratoandHeliconius melpomene. Here we quantify aspects of scale ultrastructure variation and colour in crosses between iridescent and non-iridescent subspecies of both of these species and perform quantitative trait locus (QTL) mapping. We show that iridescent structural colour has a complex genetic basis in both species, with offspring from crosses having wide variation in blue colour (both hue and brightness) and scale structure measurements. We detect two different genomic regions in each species that explain modest amounts of this variation, with a sex-linked QTL inH. eratobut notH. melpomene. We also find differences between species in the relationships between structure and colour, overall suggesting that these species have followed different evolutionary trajectories in their evolution of structural colour. We then identify genes within the QTL intervals that are differentially expressed between subspecies and/or wing regions, revealing likely candidates for genes controlling structural colour formation.
Pinhead antagonizes Admp to promote notochord formation
Authors: Itoh Keiji , Ossipova Olga , Sokol Sergei Y. 
Published: April 2021

SummaryDorsoventral patterning of a vertebrate embryo critically depends on the activity of Smad1 that mediates signaling by several BMP proteins, anti-dorsalizing morphogenetic protein (Admp), and their antagonists. Pinhead (Pnhd), a cystine-knot-containing secreted protein, is expressed in the ventrolateral marginal zone duringXenopusgastrulation, however, its molecular targets and signaling mechanisms have not been fully elucidated. An unbiased mass spectrometry-based screen of the gastrulasecretomeidentified Admp as a primary Pnhd-associated protein. We show that Pnhd binds Admp and inhibits its ventralizing activity by reducing Smad1 phosphorylation and suppressing its transcriptional targets. By contrast, Pnhd did not affect the signaling activity of BMP4. Importantly, the Admp gain-of-function phenotype and phospho-Smad1 levels have been enhanced after Pnhd depletion. Furthermore, Pnhd strongly synergized with Chordin and a truncated BMP4 receptor in the induction of notochord markers in ectoderm cells, and Pnhd-depleted embryos displayed notochord defects. Our findings suggest that Pnhd binds and inactivates Admp to promote notochord development. We propose that the interaction between Admp and Pnhd refines Smad1 activity gradients during vertebrate gastrulation.
Seismic responses to an earthquake source in stratified transversely isotropic porous media
Authors: Sun Junhua , Gao Yongxin , Tong Ping , He Xiao , Wang Wei , Geng Shuwei 
Published: April 2021

ABSTRACTIn this paper, we study seismic responses to an earthquake source in horizontally stratified transversely isotropic porous media with a vertical axis of symmetry that is, transversely isotropic porous media. We present a semi‐analytical method to simulate the three‐dimensional time–space–domain seismic wavefields. We obtain the solution in the frequency–wavenumber domain by the global matrix method and transform it to the time–space domain by the discrete wavenumber method and fast Fourier transform. Our method incorporates the moment tensor source so that it allows simulating seismic responses to an earthquake. We validate our method by degenerating the transversely isotropic porous media into the isotropic porous media and transversely isotropic solid media, respectively, and compare the results with the corresponding reference solutions. We then investigate the characteristics of seismic wavefields in the transversely isotropic porous media by considering an explosive source, a shear‐wave source and a double‐couple source. The results reveal interesting observations in the transversely isotropic porous media versus the isotropic porous media. For example, the wave can have a response to the pore pressure during its propagation in a transversely isotropic porous medium while the shear‐wave does not generate any disturbance of the pore pressure. Our method is semi‐analytical and computationally efficient and it can be used for rapid evaluation of the seismic responses in transversely isotropic porous media.
Intense nocturnal warming alters growth strategies, colouration and parasite load in a diurnal lizard
Authors: Rutschmann Alexis , Dupoué Andréaz , Miles Donald B. , Megía‐Palma Rodrigo , Lauden Clémence , Richard Murielle , Badiane Arnaud , Rozen‐Rechels David , Brevet Mathieu , Blaimont Pauline , Meylan Sandrine , Clobert Jean , Le Galliard Jean‐François 
Published: April 2021

Abstract

In the past decades, nocturnal temperatures have been playing a disproportionate role in the global warming of the planet. Yet, they remain a neglected factor in studies assessing the impact of global warming on natural populations.

Here, we question whether an intense augmentation of nocturnal temperatures is beneficial or deleterious to ectotherms. Physiological performance is influenced by thermal conditions in ectotherms and an increase in temperature by only 2°C is sufficient to induce a disproportionate increase in metabolic expenditure. Warmer nights may expand ectotherms' species thermal niche and open new opportunities for prolonged activities and improve foraging efficiency. However, increased activity may also have deleterious effects on energy balance if exposure to warmer nights reduces resting periods and elevates resting metabolic rate.

We assessed whether warmer nights affected an individual's growth, dorsal skin colouration, thermoregulation behaviour, oxidative stress status and parasite load by exposing yearling common lizards (Zootoca vivipara) from four populations to either ambient or high nocturnal temperatures for approximately 5 weeks.

Warmer nocturnal temperatures increased the prevalence of ectoparasitic infestation and altered allocation of resources towards structural growth rather than storage. We found no change in markers for oxidative stress. The thermal treatment did not influence thermal preferences, but influenced dorsal skin brightness and luminance, in line with a predicted acclimation response in colder environments to enhance heat gain from solar radiation.

Altogether, our results highlight the importance of considering nocturnal warming as an independent factor affecting ectotherms' life history in the context of global climate change.

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Patterns of striped skunk scavenging on human remains
Authors: Smith Alexander 
Published: April 2021

AbstractScavenging is a known behavior of striped skunks (Mephitis mephitis), though it is rarely documented. Striped skunks were observed and documented scavenging nine human donors at the Forensic Investigation Research Station (FIRS) in Whitewater, Colorado from October 2017 through September 2019. Human remains are placed on the surface, outdoors, in a fenced area, and monitored daily through notes, photographs, and multiple systems for scoring decomposition. Motion‐activated game cameras are strategically positioned to monitor potential scavenger activity within the facility. When scavenging occurred, game camera images were temporally correlated to daily photographs and notes to confirm the source of observed defects. Striped skunks at the FIRS scavenged the soft tissue of the arms, legs, genitals, and torso. Game camera images documented skunks digging, climbing on top of remains, repositioning limbs, and using their paws to manipulate tissue. These activities impacted soft tissue, bone, and the surrounding environment. Scavenging patterns varied seasonally, with higher frequency and lower selectivity in the winter. Striped skunks are common throughout most of North America and are likely to scavenge human remains when available. Understanding patterns and behaviors of specific scavengers can help investigators accurately interpret defects found on and around human remains.
Linkage and linkage disequilibrium among the markers in the forensic MPS panels
Authors: Li Ran , Budowle Bruce , Sun Hongyu , Ge Jianye 
Published: April 2021

AbstractFor the past two to three decades, forensic DNA evidence has been analyzed with a limited number of short tandem repeats (STRs), and these STRs are usually assumed to be independent for statistical calculations. With the development and implementation of the MPS technologies, more autosomal markers, both single nucleotide polymorphisms (SNPs) and STRs, can be analyzed. A number of these markers are physically very close to each other, and it may not be appropriate to assume all these markers are genetically unlinked or in linkage equilibrium. In this study, publicly accessible genomic data from five representative populations were used to evaluate the genetic linkage and linkage disequilibrium (LD) between autosomal markers represented in six major commercial panels (in total, 362 markers). Among the 3041 syntenic marker pairs, 1524 pairs had sex‐average genetic distances <50 cM, and thus, these marker pairs can be considered as genetically linked. Among the 143 marker pairs with physical distances <1 Mb, 19 LD haplotype blocks (comprising 39 SNPs in total) were detected for at least one of the tested populations. Statistical methods for interpreting linked markers and/or markers in LD were suggested for various case scenarios.
Using hot steam exposure to reveal mechanical properties of spaghetti beams and columns
Authors: Akbar Fathan , Abdullah Mikrajuddin 
Published: April 2021

AbstractWe demonstrate that the bending evolution of spaghetti beams and columns by hot steam reveals several food‐related properties: time‐dependent Young modulus, the diffusion coefficient of steam molecules penetrating the material, the partial Fickian behavior of molecule diffusion, and a logistic‐like evolution of the column‐bending angle. The time‐lapse images of the spaghetti strands were recorded for estimating the strand's curvatures and, from these estimates, the strand's Young's moduli were calculated. Freely hung cantilever spaghetti beams and columns were exposed to hot steam from boiling water so that the images were recorded in real time while the beam or column bent undisturbedly. It is observed that the Young modulus decreased exponentially with time after an appropriate considerable period of exposure. The diffusion coefficient of water molecules can be estimated from the bending evolution, and our data matched with the experimental data reported by others. The method presented in this paper provides an alternative method for estimating the diffusion coefficient of vapor molecules penetrating the materials.Practical ApplicationThe elastic modulus is estimated by merely measuring the angle made by the spaghetti's free end in the form of a cantilever beam or column. The measurement is performed remotely. Using a simple calculation, the error of estimation is less than 5%. The chef can use the simulated result for estimating the “doneness” of the spaghetti being boiled or steamed by clamping a piece of spaghetti horizontally and guessing the angle of the free end.
Health‐related quality of life and work impairment in idiopathic inflammatory myopathies in South Australia
Authors: Xu Alan , Sun Caitlyn , Metcalf Robert , Limaye Vidya 
Published: April 2021

AbstractAimThe idiopathic inflammatory myopathies (IIM) are rare autoimmune diseases that are usually chronic and often present with skeletal muscle inflammation and weakness. We sought to examine the impact of IIM in a cohort of 50 South Australian patients on health‐related quality of life (HRQOL) and work productivity (WP). We uniquely categorized patients across gender, IIM subtypes, employment status, and also whether there was extramuscular involvement from IIM.MethodsMultiple modalities were used, as recommended by the International Myositis Assessment and Clinical Studies Group (IMACS), to assess the impact of IIM, including manual muscle strength testing (MMT‐8), the Physician and Patient Global Activity Assessments (PHGAA, PTGAA), Myositis Disease Activity Assessment Tool (MDAAT), and serum creatinine kinase (CK) levels. The impacts of IIM on HRQOL and WP were analyzed using the Medical Outcomes Study 36‐items Short Form (SF‐36) and Work Productivity and Activity Impairment (WPAI) questionnaires, respectively.ResultsWe found significantly lower HRQOL outcome scores in most of the SF‐36 domains when compared to the most recent population norms (P ≤ .01). Physical health was predominantly affected with relative preservation of emotional health. There were also significant associations between MMT‐8, PHGAA and PTGAA scores and HRQOL and WP.ConclusionsOur findings highlight the significant impact of IIM on HRQOL and WP in a well‐characterized cohort of patients with IIM within Australia, and therefore the importance of a holistic approach to the management of these patients.
Association of FOXP3 rs3761548 polymorphism and its reduced expression with unexplained recurrent spontaneous abortions: A South Indian study
Authors: Dirsipam Kethora , Ponnala Deepika , Madduru Dhatri , Bonu Rajeswari , Jahan Parveen 
Published: April 2021

AbstractProblem: Fork Head Box Protein 3 (FOXP3) is an X‐linked gene, codes for a master transcription regulatory protein that controls the development and function of immunosuppressive T regulatory (Treg) cells. They are crucial mediators of maternal foetal tolerance and successful pregnancy outcome. The aim of the study is to evaluate the association of FOXP3 rs3761548 functional polymorphism and to assess the serum concentrations of full‐length FOXP3 protein in Unexplained Recurrent Spontaneous Abortions (URSA) patients of Southern India.Method of study: The study included blood samples from 150 URSA patients and 150 healthy, pregnant parous women. Polymerase Chain Reaction‐Restriction Fragment Length Polymorphism was done for rs3761548 FOXP3 genotyping. Serum concentrations of full‐length FOXP3 protein were estimated by enzyme‐linked immunosorbent assay.Results: The frequencies of mutant A allele, CA and AA genotypes of rs3761548 functional polymorphism were significantly elevated in patients compared to healthy, pregnant parous women and exhibited a two, three and twofold increased risk respectively towards URSA. Serum concentrations of full‐length FOXP3 protein were high in controls compared to patients (10.14 ± .30 vs. 8.84 ± 1.73 ng/ml; p < .05).Conclusion: Our results advocate an association of FOXP3 rs3761548 polymorphism and reduced expression of full‐length FOXP3 protein with URSA.
Laparoscopic surgery using 8 K ultra‐high‐definition technology: Outcomes of a phase II study
Authors: Tsukamoto Shunsuke , Kuchiba Aya , Moritani Konosuke , Shida Dai , Katayama Hiroshi , Yorikane Eiko , Kanemitsu Yukihide 
Published: April 2021

AbstractIntroductionCurrently, laparoscopic surgery generally relies on 2 K high‐definition image quality. The National Cancer Center Hospital, Olympus Corporation, and NHK Engineering System Inc. recently developed a new laparoscopic system with an 8 K ultra‐high‐definition (UHD) camera that provides images with a high‐resolution, wide color range, high frame rate, and high dynamic range. This study aimed to investigate the effectiveness and safety of a new laparoscopic system which uses an 8 K UHD camera system (8K UHD system).MethodsThis phase II study enrolled 23 patients with colon or rectosigmoid cancer who were indicated for radical resection with laparoscopic colectomy using the 8 K UHD system. The primary endpoint was the proportion of patients with ≥30 mL of intraoperative blood loss.ResultsOf the 23 patients, 22 completed laparoscopic surgery with the 8 K UHD system. One patient was converted to the 2 K high‐definition laparoscopic system due to technical difficulties with the 8 K UHD system during surgery. The median amount of intraoperative blood loss was 14 mL (range, 2‐71 mL), and number of patients with intraoperative blood loss ≥30 mL was four (17.4%). None of the patients had >100 mL of intraoperative blood loss. No intraoperative complications were noted, and four (17.4%) patients developed postoperative complications. Pathological complete resection was achieved in all patients, and no conversion to open surgery was required.ConclusionsLaparoscopic surgery using the 8 K UHD system appears to be both safe and effective. However, further refinements may be necessary to improve usability.
Feature screening with large‐scale and high‐dimensional survival data
Authors: Yi Grace Y. , He Wenqing , Carroll Raymond. J. 
Published: April 2021

AbstractData with a huge size present great challenges in modeling, inferences, and computation. In handling big data, much attention has been directed to settings with “largepsmalln”, and relatively less work has been done to address problems withpandnbeing both large, though data with such a feature have now become more accessible than before, whereprepresents the number of variables andnstands for the sample size. The big volume of data does not automatically ensure good quality of inferences because a large number of unimportant variables may be collected in the process of gathering informative variables. To carry out valid statistical analysis, it is imperative to screen out noisy variables that have no predictive value for explaining the outcome variable. In this paper, we develop a screening method for handling large‐sized survival data, where the sample sizenis large and the dimensionpof covariates is of non‐polynomial order of the sample sizen, or the so‐called NP‐dimension. We rigorously establish theoretical results for the proposed method and conduct numerical studies to assess its performance. Our research offers multiple extensions of existing work and enlarges the scope of high‐dimensional data analysis. The proposed method capitalizes on the connections among useful regression settings and offers a computationally efficient screening procedure. Our method can be applied to different situations with large‐scale data including genomic data.
“Blepharophimosis‐plus” syndromes: Frequency of systemic genetic disorders that also include blepharophimosis
Authors: Landau Prat Daphna , Nguyen Brian J. , Strong Alanna , Katowitz William R. , Katowitz James A. 
Published: April 2021

AbstractBackgroundTo determine the frequency of isolated blepharophimosis‐ptosis‐epicanthus inversus syndrome (BPES) versus systemic genetic disorders in patients presenting with blepharophimosis.MethodsRetrospective clinical records review. The records of all patients with blepharophimosis seen in the Division of Ophthalmology at the Children's Hospital of Philadelphia during a 12‐year‐period (2009‐2020) were reviewed for medical history, clinical examination findings and results of genetic analyses.ResultsThe 135 patients identified with blepharophimosis included 72 females (53%) and 63 males (47%) whose mean ± standard deviation age at first visit was 3.5 ± 6.4 years (range 0‐39.8 years). Sixty‐seven of the patients (50%) had undergone genetic testing for FOXL2 gene mutation. Fifty‐four (81%) harboured FOXL2 gene mutations and 13 (19%) did not. Altogether, 126 patients (93%) had a final diagnosis of isolated BPES. The remaining nine (7%) had syndromic diagnoses (“blepharophimosis‐plus”), including Dubowitz syndrome (n = 2), Ohdo syndrome (n = 1), 22q11.2 duplication (n = 1) and 3q22 deletion (n = 2). Three patients with multiple congenital anomalies remain undiagnosed.ConclusionsBlepharophimosis is an eyelid feature occurring most commonly in isolation due to FOXL2 gene mutation, but can also be a harbinger of multisystem disease not exclusive to isolated BPES, as observed in 7% of cases in this series. The ophthalmologist is often the first to recognise these unique features, and must consider and rule out non‐BPES syndromes before establishing a diagnosed classic BPES. A comprehensive genetic evaluation is, therefore, indicated in all cases.