bluuebunny/crossref_metadata_2025_split huggingface dataset:
Responses of turkey vultures to unmanned aircraft systems vary by platform
Authors: Pfeiffer Morgan B. , Blackwell Bradley F. , Seamans Thomas W. , Buckingham Bruce N. , Hoblet Joshua L. , Baumhardt Patrice E. , DeVault Travis L. , Fernández-Juricic Esteban 
Published: November 2021

AbstractA challenge that conservation practitioners face is manipulating behavior of nuisance species. The turkey vulture (Cathartes aura) can cause substantial damage to aircraft if struck. The goal of this study was to assess vulture responses to unmanned aircraft systems (UAS) for use as a possible dispersal tool. Our treatments included three platforms (fixed-wing, multirotor, and a predator-like ornithopter [powered by flapping flight]) and two approach types (30 m overhead or targeted towards a vulture) in an operational context. We evaluated perceived risk as probability of reaction, reaction time, flight-initiation distance (FID), vulture remaining index, and latency to return. Vultures escaped sooner in response to the fixed-wing; however, fewer remained after multirotor treatments. Targeted approaches were perceived as riskier than overhead. Vulture perceived risk was enhanced by flying the multirotor in a targeted approach. We found no effect of our treatments on FID or latency to return. Latency was negatively correlated with UAS speed, perhaps because slower UAS spent more time over the area. Greatest visual saliency followed as: ornithopter, fixed-wing, and multirotor. Despite its appearance, the ornithopter was not effective at dispersing vultures. Because effectiveness varied, multirotor/fixed-wing UAS use should be informed by management goals (immediate dispersal versus latency).
Highly sensitive low field Lorentz-force MEMS magnetometer
Authors: Mbarek Sofiane Ben , Alcheikh Nouha , Ouakad Hassen M. , Younis Mohammad I. 
Published: November 2021

AbstractWe present a highly sensitive Lorentz-force magnetic micro-sensor capable of measuring low field values. The magnetometer consists of a silicon micro-beam sandwiched between two electrodes to electrostatically induce in-plane vibration and to detect the output current. The method is based on measuring the resonance frequency of the micro-beam around the buckling zone to sense out-of-plane magnetic fields. When biased with a current of 0.91 mA (around buckling), the device has a measured sensitivity of 11.6 T−1, which is five orders of magnitude larger than the state-of-the-art. The measured minimum detectable magnetic field and the estimated resolution of the proposed magnetic sensor are 100 µT and 13.6 µT.Hz−1/2, respectively. An analytical model is developed based on the Euler–Bernoulli beam theory and the Galerkin discretization to understand and verify the micro-sensor performance. Good agreement is shown between analytical results and experimental data. Furthermore, the presented magnetometer is promising for measuring very weak biomagnetic fields.
Functional roles of the membrane-associated AAV protein MAAP
Authors: Galibert Lionel , Hyvönen Amira , Eriksson Reetta A. E. , Mattola Salla , Aho Vesa , Salminen Sami , Albers Justin D. , Peltola Sanna K. , Weman Saija , Nieminen Tiina , Ylä-Herttuala Seppo , Lesch Hanna P. , Vihinen-Ranta Maija , Airenne Kari J. 
Published: November 2021

AbstractWith a limited coding capacity of 4.7 kb, adeno-associated virus (AAV) genome has evolved over-lapping genes to maximise the usage of its genome. An example is the recently found ORF in the cap gene, encoding membrane-associated accessory protein (MAAP), located in the same genomic region as the VP1/2 unique domain, but in a different reading frame. This 13 KDa protein, unique to the dependovirus genus, is not homologous to any known protein. Our studies confirm that MAAP translation initiates from the first CTG codon found in the VP1 ORF2. We have further observed MAAP localised in the plasma membrane, in the membranous structures in close proximity to the nucleus and to the nuclear envelope by co-transfecting with plasmids encoding the wild-type AAV (wt-AAV) genome and adenovirus (Ad) helper genes. While keeping VP1/2 protein sequence identical, both inactivation and truncation of MAAP translation affected the emergence and intracellular distribution of the AAV capsid proteins. We have demonstrated that MAAP facilitates AAV replication and has a role in controlling Ad infection. Additionally, we were able to improve virus production and capsid integrity through a C-terminal truncation of MAAP while other modifications led to increased packaging of contaminating, non-viral DNA. Our results show that MAAP plays a significant role in AAV infection, with profound implications for the production of therapeutic AAV vectors.
Plasmon-induced transparency sensor for detection of minuscule refractive index changes in ultra-low index materials
Authors: Farhadi Shahriar , Miri Mehdi , Farmani Ali 
Published: November 2021

AbstractDetection of low-index materials such as aerogels and also detection of refractive index variations in these materials is still a challenging task. Here, a high figure of merit (FOM) sensor based on plasmon-induced transparency (PIT) is proposed for the detection of aerogel refractive index changes. In the proposed PIT sensor, the transparency window in an opaque region arises from the coupling between surface plasmon polariton (SPP) mode and planar waveguide mode. By comprising sub-wavelength grating (SWG) in the planar waveguide region, the maximum of the electric field of waveguide occurs in a low index media. This facilitates detection of the aerogels when they are used as the low index material (sensing material). Application of the subwavelength grating waveguide also improves the sensitivity of the sensor by a factor of six compared to a conventional structure with a homogenous waveguide. The proposed structure has a quality factor of Q ≥ 1800, and a reflection of 86%, and can detect the refractive index changes as low as Δn = 0.002 (around n = 1.0). The lineshape, Q-factor, and resonant wavelength of the transparency spectrum can be controlled by tailoring the structural parameters. Our work also has potential application in switching, filtering, and spectral shaping.
Serum HE4 and CA125 combined to predict and monitor recurrence of type II endometrial carcinoma
Authors: Quan Quan , Liao Qianqian , Yin Wanchun , Zhou Shuwei , Gong Sainan , Mu Xiaoling 
Published: November 2021

AbstractThere is no recognized serum biomarker to predict the recurrence of endometrial carcinoma (EC). We aimed to explore serum human epididymis protein 4 (HE4) and cancer antigen 125 (CA125) as the biomarkers to predict and monitor recurrence of type II EC. 191 patients diagnosed with type II EC were involved for this retrospective study. Comparing recurrent with non-recurrent patients, HE4 levels resulted a statistically significant difference at primary diagnosis and recurrence, respectively (P = 0.002 and P = < 0.001), while CA125 levels resulted statistically significant (P = < 0.001) at recurrence. According to receiver operating characteristic curve analysis, the areas under the curve were significant for HE4 levels at primary diagnosis and recurrence predicting recurrence. Furthermore, CA125 levels at recurrence were significant. And the combination of both markers showed the higher sensitivity and specificity than single one. Patients with higher HE4 levels were associated with worse disease-free survival and overall survival, the opposite was true for patients with lower HE4 levels. The preoperative HE4 levels could be used to evaluate the risk factors of type II EC. Which suggested that HE4 levels might associated with the prognosis of type II EC. And combination of HE4 and CA125 could be applied to monitor recurrence during follow-up.
Design considerations for workflow management systems use in production genomics research and the clinic
Authors: Ahmed Azza E. , Allen Joshua M. , Bhat Tajesvi , Burra Prakruthi , Fliege Christina E. , Hart Steven N. , Heldenbrand Jacob R. , Hudson Matthew E. , Istanto Dave Deandre , Kalmbach Michael T. , Kapraun Gregory D. , Kendig Katherine I. , Kendzior Matthew Charles , Klee Eric W. , Mattson Nate , Ross Christian A. , Sharif Sami M. , Venkatakrishnan Ramshankar , Fadlelmola Faisal M. , Mainzer Liudmila S. 
Published: November 2021

AbstractThe changing landscape of genomics research and clinical practice has created a need for computational pipelines capable of efficiently orchestrating complex analysis stages while handling large volumes of data across heterogeneous computational environments. Workflow Management Systems (WfMSs) are the software components employed to fill this gap. This work provides an approach and systematic evaluation of key features of popular bioinformatics WfMSs in use today: Nextflow, CWL, and WDL and some of their executors, along with Swift/T, a workflow manager commonly used in high-scale physics applications. We employed two use cases: a variant-calling genomic pipeline and a scalability-testing framework, where both were run locally, on an HPC cluster, and in the cloud. This allowed for evaluation of those four WfMSs in terms of language expressiveness, modularity, scalability, robustness, reproducibility, interoperability, ease of development, along with adoption and usage in research labs and healthcare settings. This article is trying to answer,which WfMS should be chosen for a given bioinformatics application regardless of analysis type?. The choice of a given WfMS is a function of both its intrinsic language and engine features. Within bioinformatics, where analysts are a mix of dry and wet lab scientists, the choice is also governed by collaborations and adoption within large consortia and technical support provided by the WfMS team/community. As the community and its needs continue to evolve along with computational infrastructure, WfMSs will also evolve, especially those with permissive licenses that allow commercial use. In much the same way as the dataflow paradigm and containerization are now well understood to be very useful in bioinformatics applications, we will continue to see innovations of tools and utilities for other purposes, like big data technologies, interoperability, and provenance.
Features and applications of haplotypes in crop breeding
Authors: Bhat Javaid Akhter , Yu Deyue , Bohra Abhishek , Ganie Showkat Ahmad , Varshney Rajeev K. 
Published: November 2021

AbstractClimate change with altered pest-disease dynamics and rising abiotic stresses threatens resource-constrained agricultural production systems worldwide. Genomics-assisted breeding (GAB) approaches have greatly contributed to enhancing crop breeding efficiency and delivering better varieties. Fast-growing capacity and affordability of DNA sequencing has motivated large-scale germplasm sequencing projects, thus opening exciting avenues for mining haplotypes for breeding applications. This review article highlights ways to mine haplotypes and apply them for complex trait dissection and in GAB approaches including haplotype-GWAS, haplotype-based breeding, haplotype-assisted genomic selection. Improvement strategies that efficiently deploy superior haplotypes to hasten breeding progress will be key to safeguarding global food security.
Truncating tau reveals different pathophysiological actions of oligomers in single neurons
Authors: Hill Emily , Karikari Thomas K. , Lantero-Rodriguez Juan , Zetterberg Henrik , Blennow Kaj , Richardson Magnus J. , Wall Mark J. 
Published: November 2021

AbstractTau protein is involved in maintaining neuronal structure. In Alzheimer’s disease, small numbers of tau molecules can aggregate to form oligomers. However, how these oligomers produce changes in neuronal function remains unclear. Previously, oligomers made from full-length human tau were found to have multiple effects on neuronal properties. Here we have cut the tau molecule into two parts: the first 123 amino acids and the remaining 124-441 amino acids. These truncated tau molecules had specific effects on neuronal properties, allowing us to assign the actions of full-length tau to different regions of the molecule. We identified one key target for the effects of tau, the voltage gated sodium channel, which could account for the effects of tau on the action potential. By truncating the tau molecule, we have probed the mechanisms that underlie tau dysfunction, and this increased understanding of tau’s pathological actions will build towards developing future tau-targeting therapies.
Mitochondrial-nuclear cross-talk in the human brain is modulated by cell type and perturbed in neurodegenerative disease
Authors: Fairbrother-Browne Aine , Ali Aminah T. , Reynolds Regina H. , Garcia-Ruiz Sonia , Zhang David , Chen Zhongbo , Ryten Mina , Hodgkinson Alan 
Published: November 2021

AbstractMitochondrial dysfunction contributes to the pathogenesis of many neurodegenerative diseases. The mitochondrial genome encodes core respiratory chain proteins, but the vast majority of mitochondrial proteins are nuclear-encoded, making interactions between the two genomes vital for cell function. Here, we examine these relationships by comparing mitochondrial and nuclear gene expression across different regions of the human brain in healthy and disease cohorts. We find strong regional patterns that are modulated by cell-type and reflect functional specialisation. Nuclear genes causally implicated in sporadic Parkinson’s and Alzheimer’s disease (AD) show much stronger relationships with the mitochondrial genome than expected by chance, and mitochondrial-nuclear relationships are highly perturbed in AD cases, particularly through synaptic and lysosomal pathways, potentially implicating the regulation of energy balance and removal of dysfunction mitochondria in the etiology or progression of the disease. Finally, we presentMitoNuclearCOEXPlorer, a tool to interrogate key mitochondria-nuclear relationships in multi-dimensional brain data.
Quantifying cell-generated forces: Poisson’s ratio matters
Authors: Javanmardi Yousef , Colin-York Huw , Szita Nicolas , Fritzsche Marco , Moeendarbary Emad 
Published: November 2021

AbstractQuantifying mechanical forces generated by cellular systems has led to key insights into a broad range of biological phenomena from cell adhesion to immune cell activation. Traction force microscopy (TFM), the most widely employed force measurement methodology, fundamentally relies on knowledge of the force-displacement relationship and mechanical properties of the substrate. Together with the elastic modulus, the Poisson’s ratio is a basic material property that to date has largely been overlooked in TFM. Here, we evaluate the sensitivity of TFM to Poisson’s ratio by employing a series of computer simulations and experimental data analysis. We demonstrate how applying the correct Poisson’s ratio is important for accurate force reconstruction and develop a framework for the determination of error levels resulting from the misestimation of the Poisson’s ratio. In addition, we provide experimental estimation of the Poisson’s ratios of elastic substrates commonly applied in TFM. Our work thus highlights the role of Poisson’s ratio underpinning cellular force quantification studied across many biological systems.
High-dose dexamethasone injection disordered metabolism and multiple protein kinases expression in the mouse kidney
Authors: Zhang Zaikuan , Ran Yingchun , Xu Lei , Pan Zheng , Xie Yajun 
Published: November 2021

Abstract
Glucocorticoids (GCs) have been widely used in clinical treatment as anti-inflammatory, anti-shock and immunosuppressive medicines. However, the effect of excessive GCs on immune response and metabolism of kidney remains unclear. Here, we profiled the gene expression of kidney from mice with high-dose dexamethasone (DEX) treatment. A total of 1193 differentially expressed genes (DEGs) were screened in DEX treatment group compared with the saline group, including 715 down- regulated and 478 up-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of these DEGs showed extracellular matrix (ECM)–receptor interaction, cell adhesion molecules signaling pathway were significantly enriched, and that the vast majority of DEGs were involved in monocarboxylic acid metabolism, leukocyte cell–cell adhesion and fatty acid metabolism. Gene set enrichment analysis (GSEA) revealed that DEGs were strongly associated with immune-response and cell adhesion gene sets, such as Fc γ R-mediated phagocytosis, leukocyte transendothelial migration, T-cell receptor signaling pathway, cell adhesion, ECM–receptor interaction and focal adhesion-associated pathways. KEGG pathway analysis of differentially expressed kinases (DEKs) showed T-cell receptor and forkhead box class O signaling pathway were enriched. Furthermore, we found multiple protein kinases expression were dysregulated greatly after dexamethasone treatment, including classical effector of GCs stimulation-serum and GC-regulated kinase. These protein kinases are involved in multiple signaling pathways in mice kidney, such as mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K)/Akt signaling pathway. We profiled the gene expression of the kidney from high-dose dexamethasone-treated mice and provided important information for further study the mechanism of side effects of GCs in clinical therapy.
Objective Laryngoscopic Measures From Older Patients With Voice Complaints and Signs of Aging
Authors: Stager Sheila V. , Gupta Simran , Amdur Richard , Bielamowicz Steven A. 
Published: November 2021

Purpose:The purpose of this study was to use objective measures of glottal gap, bowing, and supraglottic compression from selected images of laryngoscopic examinations from adults over 60 years of age with voice complaints and signs of aging to test current hypotheses on whether degree of severity impacts treatment recommendations and potential follow-through with treatment.Method:Records from 108 individuals 60 years or older with voice complaints and signs of aging were reviewed. Three objective measures (normalized glottal gap area [NGGA], total bowing index, and normalized true vocal fold width) were derived. Each measure was subsequently divided into three categories by severity: absence, small degree, or large degree. Nonparametric statistics tested associations between severity and treatment recommendations as well as potential follow-through.Results:Noninvasive treatments (observation/voice therapy) were marginally associated with no glottal gap (p= .09). More invasive treatments (injection/bilateral thyroplasty) were associated with glottal gaps being present (p= .026), but bilateral thyroplasty recommendations were not significantly associated with the largest gaps. Treatment modalities were not characterized by specific severity categories for any of the objective measures. No significant differences were found for any of the three objective measures between those who followed through with recommended treatment and those who did not.Discussion:Results demonstrated some support for current hypotheses on how degrees of severity of objective measures relate to treatment recommendations. Of the three measures, NGGA appears to be more informative regarding treatment recommendations and follow-through, but due to low power, larger sample sizes are needed to confirm clinical relevance.
Event-Related Potentials Elicited by Phonetic Errors Differentiate Children With Speech Sound Disorder and Typically Developing Peers
Authors: Gerwin Katelyn L. , Brosseau-Lapré Françoise , Weber Christine 
Published: November 2021

Purpose:
A growing body of research suggests that a deficit in speech perception abilities contributes to the development of speech sound disorder (SSD). However, little work has been done to characterize the neurophysiological processes indexing speech perception deficits in this population. The primary aim of this study was to compare the neural activity underlying speech perception in young children with SSD and with typical development (TD).

Method:
Twenty-eight children ages 4;1–6;0 (years;months) participated in this study. Event-related potentials (ERPs) were recorded while children completed a speech perception task that included phonetic (speech sound) and lexical (meaning) matches and mismatches. Groups were compared on their judgment accuracy for matches and mismatches as well as the mean amplitude of the phonological mapping negativity (PMN) and N400 ERP components.

Results:
Children with SSD demonstrated lower judgment accuracy across the phonetic and lexical conditions compared to peers with TD. The ERPs elicited by lexical matches and mismatches did not distinguish the groups. However, in the phonetic condition, the SSD group exhibited a more consistent left-lateralized PMN effect and a delayed N400 effect over frontal sites compared to the TD group.

Conclusions:
These findings provide some of the first evidence of a delay in the neurophysiological processing of phonological information for young children with SSD compared to their peers with TD. This delay was not present for the processing of lexical information, indicating a unique difference between children with SSD and with TD related to speech perception of phonetic errors.

Supplemental Material

https://doi.org/10.23641/asha.16915579
Reactions of 1-Trifluoromethylprop-2-yne 1-Iminium Salts with Nitroanilines: Synthesis of 4-Trifluoromethylnitroquinolines and 1,2,3-Trisubstituted 5-Trifluoromethylpyrroles
Authors: Maas Gerhard , Seitz Bianca , Schneider Thomas , Majstorovic Nikola , Fleischmann Maximilian 
Published: November 2021

AbstractA variety of 4-trifluoromethylquinolines bearing an aryl (or cyclopropyl, tert-butyl, trimethylsilyl) group at C-2 and a nitro group at ring position 6, 7 or 8 have been prepared in good to high yields from 3-substituted 1-(trifluoromethyl)prop-2-yne 1-iminium triflate salts and o-, m- or p-nitroaniline. These reactions include an aza-Michael reaction at room temperature followed by an intramolecular electrophilic aromatic substitution step, which requires additional thermal activation in most cases. In contrast, the conjugate addition of 2,4-dinitroanilines at the acetylenic iminium ions proceeds much more slowly and some of the adducts can be converted thermally into 2-(2,4-dinitrophenyl)-5-trifluoromethylpyrroles. Analogously, 2-(4-pyridyl)-5-trifluoromethylpyrroles were obtained from 3-aryl-1-(trifluoromethyl)propyn­iminium salts and 4-aminopyridinium triflate. A novel variation of the Truce–Smiles rearrangement is probably involved in the formation of these pyrroles.
A photoionized pulsed low-energy ion beam source for quantum state-to-state crossed ion-molecule scattering
Authors: Zhang Guodong , Guan Lichang , Cheng Min , Gao Hong 
Published: November 2021

Here, we report the design and test of a pulsed low-energy ion beam source for crossed ion-molecule scattering studies. The ions are produced by laser photoionization based methods and thus can be prepared in well-defined quantum states. By using the combination of a double Einzel lenses setup and a specially designed shielding tube, a well spatially confined ion bunch with tunable kinetic energies in the range of 1.0–5.0 eV and typical spreads of ∼150 meV (full width at half maximum) can be formed in the center of a velocity-map imaging (VMI) stack. By combining it with a recently constructed three-dimensional VMI system, the present apparatus is readily available for quantum state-to-state crossed ion-molecule scattering studies.