bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum variational algorithms are swamped with traps
Authors: Anschuetz Eric R. , Kiani Bobak T. 
Published: December 2022

AbstractOne of the most important properties of classical neural networks is how surprisingly trainable they are, though their training algorithms typically rely on optimizing complicated, nonconvex loss functions. Previous results have shown that unlike the case in classical neural networks, variational quantum models are often not trainable. The most studied phenomenon is the onset of barren plateaus in the training landscape of these quantum models, typically when the models are very deep. This focus on barren plateaus has made the phenomenon almost synonymous with the trainability of quantum models. Here, we show that barren plateaus are only a part of the story. We prove that a wide class of variational quantum models—which are shallow, and exhibit no barren plateaus—have only a superpolynomially small fraction of local minima within any constant energy from the global minimum, rendering these models untrainable if no good initial guess of the optimal parameters is known. We also study the trainability of variational quantum algorithms from a statistical query framework, and show that noisy optimization of a wide variety of quantum models is impossible with a sub-exponential number of queries. Finally, we numerically confirm our results on a variety of problem instances. Though we exclude a wide variety of quantum algorithms here, we give reason for optimism for certain classes of variational algorithms and discuss potential ways forward in showing the practical utility of such algorithms.
Structural insights into p300 regulation and acetylation-dependent genome organisation
Authors: Ibrahim Ziad , Wang Tao , Destaing Olivier , Salvi Nicola , Hoghoughi Naghmeh , Chabert Clovis , Rusu Alexandra , Gao Jinjun , Feletto Leonardo , Reynoird Nicolas , Schalch Thomas , Zhao Yingming , Blackledge Martin , Khochbin Saadi , Panne Daniel 
Published: December 2022

AbstractHistone modifications are deposited by chromatin modifying enzymes and read out by proteins that recognize the modified state. BRD4-NUT is an oncogenic fusion protein of the acetyl lysine reader BRD4 that binds to the acetylase p300 and enables formation of long-range intra- and interchromosomal interactions. We here examine how acetylation reading and writing enable formation of such interactions. We show that NUT contains an acidic transcriptional activation domain that binds to the TAZ2 domain of p300. We use NMR to investigate the structure of the complex and found that the TAZ2 domain has an autoinhibitory role for p300. NUT-TAZ2 interaction or mutations found in cancer that interfere with autoinhibition by TAZ2 allosterically activate p300. p300 activation results in a self-organizing, acetylation-dependent feed-forward reaction that enables long-range interactions by bromodomain multivalent acetyl-lysine binding. We discuss the implications for chromatin organisation, gene regulation and dysregulation in disease.
Achieving single nucleotide sensitivity in direct hybridization genome imaging
Authors: Wang Yanbo , Cottle W. Taylor , Wang Haobo , Gavrilov Momcilo , Zou Roger S. , Pham Minh-Tam , Yegnasubramanian Srinivasan , Bailey Scott , Ha Taekjip 
Published: December 2022

AbstractDirect visualization of point mutations in situ can be informative for studying genetic diseases and nuclear biology. We describe a direct hybridization genome imaging method with single-nucleotide sensitivity, single guide genome oligopaint via local denaturation fluorescence in situ hybridization (sgGOLDFISH), which leverages the high cleavage specificity of eSpCas9(1.1) variant combined with a rationally designed guide RNA to load a superhelicase and reveal probe binding sites through local denaturation. The guide RNA carries an intentionally introduced mismatch so that while wild-type target DNA sequence can be efficiently cleaved, a mutant sequence with an additional mismatch (e.g., caused by a point mutation) cannot be cleaved. Because sgGOLDFISH relies on genomic DNA being cleaved by Cas9 to reveal probe binding sites, the probes will only label the wild-type sequence but not the mutant sequence. Therefore, sgGOLDFISH has the sensitivity to differentiate the wild-type and mutant sequences differing by only a single base pair. Using sgGOLDFISH, we identify base-editor-modified and unmodified progeroid fibroblasts from a heterogeneous population, validate the identification through progerin immunofluorescence, and demonstrate accurate sub-nuclear localization of point mutations.
Decoupling light absorption and carrier transport via heterogeneous doping in Ta3N5 thin film photoanode
Authors: Xiao Yequan , Fan Zeyu , Nakabayashi Mamiko , Li Qiaoqiao , Zhou Liujiang , Wang Qian , Li Changli , Shibata Naoya , Domen Kazunari , Li Yanbo 
Published: December 2022

AbstractThe trade-off between light absorption and carrier transport in semiconductor thin film photoelectrodes is a major limiting factor of their solar-to-hydrogen efficiency for photoelectrochemical water splitting. Herein, we develop a heterogeneous doping strategy that combines surface doping with bulk gradient doping to decouple light absorption and carrier transport in a thin film photoelectrode. Taking La and Mg doped Ta3N5 thin film photoanode as an example, enhanced light absorption is achieved by surface La doping through alleviating anisotropic optical absorption, while efficient carrier transport in the bulk is maintained by the gradient band structure induced by gradient Mg doping. Moreover, the homojunction formed between the La-doped layer and the gradient Mg-doped layer further promotes charge separation. As a result, the heterogeneously doped photoanode yields a half-cell solar-to-hydrogen conversion efficiency of 4.07%, which establishes Ta3N5 as a leading performer among visible‐light‐responsive photoanodes. The heterogeneous doping strategy could be extended to other semiconductor thin film light absorbers to break performance trade-offs by decoupling light absorption and carrier transport.
Cardiopulmonary examinations of athletes returning to high-intensity sport activity following SARS-CoV-2 infection
Authors: Babity Mate , Zamodics Mark , Konig Albert , Kiss Anna Reka , Horvath Marton , Gregor Zsofia , Rakoczi Reka , Kovacs Eva , Fabian Alexandra , Tokodi Marton , Sydo Nora , Csulak Emese , Juhasz Vencel , Lakatos Balint Karoly , Vago Hajnalka , Kovacs Attila , Merkely Bela , Kiss Orsolya 
Published: December 2022

AbstractAfter SARS-CoV-2 infection, strict recommendations for return-to-sport were published. However, data are insufficient about the long-term effects on athletic performance. After suffering SARS-CoV-2 infection, and returning to maximal-intensity trainings, control examinations were performed with vita-maxima cardiopulmonary exercise testing (CPET). From various sports, 165 asymptomatic elite athletes (male: 122, age: 20y (IQR: 17-24y), training:16 h/w (IQR: 12–20 h/w), follow-up:93.5 days (IQR: 66.8–130.0 days) were examined. During CPET examinations, athletes achieved 94.7 ± 4.3% of maximal heart rate, 50.9 ± 6.0 mL/kg/min maximal oxygen uptake (V̇O2max), and 143.7 ± 30.4L/min maximal ventilation. Exercise induced arrhythmias (n = 7), significant horizontal/descending ST-depression (n = 3), ischemic heart disease (n = 1), hypertension (n = 7), slightly elevated pulmonary pressure (n = 2), and training-related hs-Troponin-T increase (n = 1) were revealed. Self-controlled CPET comparisons were performed in 62 athletes: due to intensive re-building training, exercise time, V̇O2max and ventilation increased compared to pre-COVID-19 results. However, exercise capacity decreased in 6 athletes. Further 18 athletes with ongoing minor long post-COVID symptoms, pathological ECG (ischemic ST-T changes, and arrhythmias) or laboratory findings (hsTroponin-T elevation) were controlled. Previous SARS-CoV-2-related myocarditis (n = 1), ischaemic heart disease (n = 1), anomalous coronary artery origin (n = 1), significant ventricular (n = 2) or atrial (n = 1) arrhythmias were diagnosed. Three months after SARS-CoV-2 infection, most of the athletes had satisfactory fitness levels. Some cases with SARS-CoV-2 related or not related pathologies requiring further examinations, treatment, or follow-up were revealed.
lncRNA–disease association prediction method based on the nearest neighbor matrix completion model
Authors: Du Xiao-xin , Liu Yan , Wang Bo , Zhang Jian-fei 
Published: December 2022

AbstractState-of-the-art medical studies proved that long noncoding ribonucleic acids (lncRNAs) are closely related to various diseases. However, their large-scale detection in biological experiments is problematic and expensive. To aid screening and improve the efficiency of biological experiments, this study introduced a prediction model based on the nearest neighbor concept for lncRNA–disease association prediction. We used a new similarity algorithm in the model that fused potential associations. The experimental validation of the proposed algorithm proved its superiority over the available Cosine, Pearson, and Jaccard similarity algorithms. Satisfactory results in the comparative leave-one-out cross-validation test (with AUC = 0.96) confirmed its excellent predictive performance. Finally, the proposed model’s reliability was confirmed by performing predictions using a new dataset, yielding AUC = 0.92.
COVID-19 infection and vaccine have no impact on in-vitro fertilization (IVF) outcome
Authors: Albeitawi Soha , Al-Alami Zina M. , Hamadneh Jehan , Alqam Hiba , Qublan Hussein , Al Natsheh Maha 
Published: December 2022

AbstractTo investigate the effect of COVID-19 infection or vaccine on IVF outcome. This is a multicenter retrospective study. Data were collected from all patients treated in the ART units between September and November 2021 after the vaccination of the general population began. Medical records of all patients who had IVF/intracytoplasmic sperm injection (ICSI) were retrospectively reviewed. Patients were categorized into four groups: previously infected by COVID-19, vaccinated by COVID vaccine, previously infected and vaccinated, or neither infected nor vaccinated. Total number of participants 151 (vaccinated only 66, infected only 18, vaccinated and previously infected 34, and control 33. Outcomes (ET on day of trigger, number of oocytes retrieved, quality of oocytes, number of fertilized oocytes, number and quality of embryos, number of embryos transferred, number of embryos frozen, implantation rate and clinical pregnancy rate) were compared between these four groups. Moreover, we compared the outcome before and post infection, as well as before and post vaccine in a group of patients. No evidence was found to suggest that COVID-19 disease or SARS-CoV-2 Vaccine adversely affects Clinical pregnancy rates (positive fetal heartbeat) (OR 0.9, CI 0.5–1.9, OR 1.8, CI 0.9–3.6, respectively) and the following parameters: fertilization rate, implantation rate, positive bHcg) (OR 0.9, CI 0.5–1.8, OR 1.5, CI 0.7–2.9, respectively). Although a limitation of our study is the small comparison groups, and the wide confidence intervals in the Odds Ratio estimates.
Ultracompact single-layer optical MEMS accelerometer based on evanescent coupling through silicon nanowaveguides
Authors: Xin Chenguang , Zhang Zhongyao , Wang Xuhu , Fan Changjiang , Li Mengwei 
Published: December 2022

AbstractIn this paper, a novel optical MEMS accelerometer is proposed based on evanescent coupling between parallel silicon nanowaveguides. The coupling length between nanowaveguides changes due to the input acceleration, leading to a great change of coupling efficiency. As a result, the applied acceleration can be obtained by measuring the transmission of waveguiding light. Simulation results with optical displacement sensing sensitivity of 32.83%/$$\upmu $$
μ
m within measurement range of 1.68 g is obtained. This design shows high compactness with no need of assembly, suggesting great potential in applications such as integrated photonic circuits.
Controlling anammox speciation and biofilm attachment strategy using N-biotransformation intermediates and organic carbon levels
Authors: Lu Yang , Natarajan Gayathri , Nguyen Thi Quynh Ngoc , Thi Sara Swa , Arumugam Krithika , Seviour Thomas , Williams Rohan B. H. , Wuertz Stefan , Law Yingyu 
Published: December 2022

AbstractConventional nitrogen removal in wastewater treatment requires a high oxygen and energy input. Anaerobic ammonium oxidation (anammox), the single-step conversion of ammonium and nitrite to nitrogen gas, is a more energy and cost effective alternative applied extensively to sidestream wastewater treatment. It would also be a mainstream treatment option if species diversity and physiology were better understood. Anammox bacteria were enriched up to 80%, 90% and 50% relative abundance, from a single inoculum, under standard enrichment conditions with either stepwise-nitrite and ammonia concentration increases (R1), nitric oxide supplementation (R2), or complex organic carbon from mainstream wastewater (R3), respectively. Candidatus Brocadia caroliniensis predominated in all reactors, but a shift towards Ca. Brocadia sinica occurred at ammonium and nitrite concentrations > 270 mg NH4–N L−1 and 340 mg NO2–N L−1 respectively. With NO present, heterotrophic growth was inhibited, and Ca. Jettenia coexisted with Ca. B. caroliniensis before diminishing as nitrite increased to 160 mg NO2–N L−1. Organic carbon supplementation led to the emergence of heterotrophic communities that coevolved with Ca. B. caroliniensis. Ca. B. caroliniensis and Ca. Jettenia preferentially formed biofilms on surfaces, whereas Ca. Brocadia sinica formed granules in suspension. Our results indicate that multiple anammox bacteria species co-exist and occupy sub-niches in anammox reactors, and that the dominant population can be reversibly shifted by, for example, changing nitrogen load (i.e. high nitrite concentration favors Ca. Brocadia caroliniensis). Speciation has implications for wastewater process design, where the optimum cell immobilization strategy (i.e. carriers vs granules) depends on which species dominates.
Effect of vibration during bulk and incremental filling on adaptation of a bulk-fill composite resin
Authors: Kim Yung-Soo , Baek Seung-Ho , Kim Ryan Jin Young 
Published: December 2022

AbstractThis study evaluated the effect of vibration on adaptation of bulk-fill composite resin. A scanning laser doppler vibrometer measured the frequency and amplitude of a vibratory device (COMO; B&L Biotech) used for resin placement and visualized its effect on the resin according to depth. A bulk-fill composite resin (Filtek Bulk Fill; 3M ESPE) was placed in simulated cavities (4 mm diameter, 4 mm depth) by different layering methods (incremental filling with two 2-mm-thick layers vs. bulk filling with a single 4-mm-thick layer). The groups were further divided based on the application of vibration during restoration (no vibration vs. vibration). In addition to the surface void area at the cavity floor, the overall void volume and the void volumes of the bottom, middle, and top thirds were obtained for micro-computed tomography analysis. The frequency and amplitude of the COMO were approximately 149 Hz and between 26 and 51 µm, respectively. When vibration was not applied, incremental filling had a lower void volume in the bottom third of the cavity than did bulk filling (p < 0.05). Vibration applied with a 4-mm-thick bulk fill had no significant effect on the adaptation of composite resin (p > 0.05). In contrast, vibration reduced the amount of void formation in the bottom third of the cavity during incremental filling (p < 0.05). Application of vibration to resin with a 2-mm incremental-layering technique formed a smaller void at the interface between the cavity and resin and within the bulk-fill composite resin.
Analysis of disordered abrasive scratches on titanium surfaces and their impact on nuclear translocation of yes-associated protein
Authors: Migita Satoshi , Wakabayashi Keita 
Published: December 2022

AbstractThe morphology of the metallic surface of an implant is important for its contact with bone tissue as it directly affects osteoblast functions, such as cell adhesion, proliferation, and differentiation. Firm contact between the implant and cells creates a barrier that prevents inflammation and bacterial infections. Therefore, optimizing surface morphology, such as surface roughness adjustments, is essential to improving the adhesion between the implant and cells for successful tissue regeneration. However, the manner in which the cells sense the surface roughness and morphology remains unclear. Previously, we analyzed cell adhesion behavior and observed that inhibited cell spreading can delay osteoblast functions. Therefore, assuming that the surface morphology can be sensed through cell spreading, we investigated the cell spreading area and yes-associated protein (YAP) localization in mouse osteoblasts (MC3T3-E1) on a titanium surface with disordered abrasive scratches. Surface roughness of 100–150 nm was obtained by polishing, which inhibited the cell spreading, indicating that YAP localization in the nucleus was lower than that on other surfaces. The obtained results indicate that the cells sense the surface environment based on their spreading area, which regulates cellular functions via the Hippo pathway.
Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Allium mongolicum
Authors: Jin Yanan , Zhang Ting , Liu Binke , Zheng Chengzhong , Huo Hongyan , Zhang Jixing 
Published: December 2022

AbstractAllium mongolicum Regel is a wild and sandy vegetable with unique flavours. In this study, a complete chloroplast (cp) genome of A. mongolicum was obtained (Genbank accession number: OM630416), and contained 153,609 base pairs with the GC ratio as 36.8%. 130 genes were annotated including 84 protein-coding genes, 38 tRNA, and 8 rRNA genes. The large single-copy (LSC) region was 82,644 bp, and a small single-copy (SSC) region was 18,049 bp, which were separated by two inverted repeats (IRs, including IRa and IRb) of 26,458 bp. Comparative genome analyses of 55 Allium species suggested that genomic structure of genus Allium was conserved, and LSC and SSC regions were outstanding with high variability. Among them, more divergent loci were in the SSC region covering ycf1-rrn4.5 and ndhF-ccsA. Phylogenetic analysis on cp genomes of 55 Allium determined that all members were clustered into 13 clades, and A. mongolicum had close relationship with A. senescens. Corresponding analyses of four protein-coding genes (ycf1, ndhF, rpl32, and ccsA) in aforementioned divergent loci confirmed that ycf1 was finally chosen as the candidate gene for species identification and evolutionary classification of genus Allium. These data provide valuable genetic resources for future research on Allium.
The ultraluminous X-ray source M 81 X-6: a weakly magnetised neutron star with a precessing accretion disc?
Authors: Amato R. , Gúrpide A. , Webb N. A. , Godet O. , Middleton M. J. 
Published: December 2022

Context. Thanks to their proximity, ultraluminous X-ray sources (ULXs) represent a privileged astrophysical laboratory to study super-Eddington accretion. Current open questions concern the nature of the compact object, which is still hard to determine in those cases where pulsations are not directly detected, and the mechanisms responsible for the spectral changes observed in many ULXs.
Aims. We investigate the nature of the ULX M 81 X-6, which has been suggested to harbour a neutron star (NS), by studying its long-term X-ray spectral and temporal evolution, with the goal of assessing the astrophysical phenomena responsible for its spectral changes.
Methods. Using the rich set of available archival data from XMM-Newton, Chandra, NuSTAR, and Swift/XRT, we tracked the evolution of the source on the hardness-intensity diagram and inferred the different emitting regions of the system and their geometry, as well as the mechanisms responsible for the spectral transitions.
Results. We find that the source oscillates between two main states: one characterised by a hard and luminous spectrum and the other at low hardness and luminosity. The properties of the soft component remain constant between the two states, suggesting that changes in the mass-transfer rate are not driving the spectral transitions. Instead, the bi-modal behaviour of the source and the known super-orbital period would point to the precession of the accretion disc. Here, we tested two theoretical models: (1) Lense-Thirring precession, which can explain the super-orbital period if the NS has a magnetic field B ≲ 1010 G, supporting the idea of M 81 X-6 as a weakly magnetised NS, and (2) precession due to the torque of the NS magnetic field, which leads to B ≳ 1011 G. However, the latter scenario, assuming M 81 X-6 shares similar properties with other NS-ULXs, is disfavoured because it would require magnetic field strengths (B > 1015 G) much higher than those known for other pulsating ULXs. We further show that the contribution from the hard component attributed to the putative accretion column sits just below the typical values found in pulsating ULXs, which, together with the low value of the pulsed fraction (≤10%) found for one XMM-Newton/pn observation, could explain the source’s lack of pulsations.
Conclusions. The spectral properties and variability of M 81 X-6 can be accounted for if the accretor is a NS with a low magnetic field. Under the hypothesis of Lense-Thirring precession, we predict a spin period of the NS of a few seconds. We encourage future X-ray pointed observations to look for pulsations and/or spectral signatures of the magnetic field.
An integrated Hardware/Software Verification and Validation methodology for Signal Processing Systems
Authors: Venugopal Manokar , Nanda Manju , Anand G. , Chandana Voora Hari 
Published: December 2022

The testing and validation services team assesses project deliverables at various stages of development using innovative and effective verification and validation, to ensure that the deliverables are compliance with the customer specifications and requirements. Whenever new products and devices are released, completely integrated verification and validation services are delivered to accurate and complete records usability, performance, and quality assurance services. Throughout the product development and testing process, the testing and validation services team employs verification and validation techniques. Code reviews, walk through, inspections, desk-checking, and code execution are all examples of verification and validation techniques. Services for verification and validation are used to assess whether or not the software or application provided complies with the requirements and serves the intended purpose. A procedure used to ensure that the software created is of good quality and consistently operates as expected is independent testing and validation services. Unit testing (also known as “White Box Testing”), hardware-software integration testing (HSIT), and system testing are the three primary independent verification and validation approaches (Black Box Testing). The teams responsible for the verification and validation services actively participate in each stage of the project and design the services according to the project’s needs (e.g., prototype, spiral, iterative, V Model, and Agile). Our expertise in the embedded domain, tried-and-true verification and validation techniques, and a thorough methodology provide a quick turnaround and excellent results for the targeted solution.
Independent Verification and validation services covering

Source code, design, and requirements
White box testing, or unit testing
Testing for hardware-software integration
Black box testing, or system testing
To reduce test cycle-time significantly on test Automation solutions.
Verification and validation techniques can be used to effectively and efficiently carry out stress and performance tests, and to detect defects early in the life cycle.
Documentation of test process.
Liaison and Certification