bluuebunny/crossref_metadata_2025_split huggingface dataset:
A catalogue of biochemically diverse CRISPR-Cas9 orthologs
Authors: Gasiunas Giedrius , Young Joshua K. , Karvelis Tautvydas , Kazlauskas Darius , Urbaitis Tomas , Jasnauskaite Monika , Grusyte Mantvyda M. , Paulraj Sushmitha , Wang Po-Hao , Hou Zhenglin , Dooley Shane K. , Cigan Mark , Alarcon Clara , Chilcoat N. Doane , Bigelyte Greta , Curcuru Jennifer L. , Mabuchi Megumu , Sun Zhiyi , Fuchs Ryan T. , Schildkraut Ezra , Weigele Peter R. , Jack William E. , Robb G. Brett , Venclovas Česlovas , Siksnys Virginijus 
Published: November 2020

AbstractBacterial Cas9 nucleases from type II CRISPR-Cas antiviral defence systems have been repurposed as genome editing tools. Although these proteins are found in many microbes, only a handful of variants are used for these applications. Here, we use bioinformatic and biochemical analyses to explore this largely uncharacterized diversity. We apply cell-free biochemical screens to assess the protospacer adjacent motif (PAM) and guide RNA (gRNA) requirements of 79 Cas9 proteins, thus identifying at least 7 distinct gRNA classes and 50 different PAM sequence requirements. PAM recognition spans the entire spectrum of T-, A-, C-, and G-rich nucleotides, from single nucleotide recognition to sequence strings longer than 4 nucleotides. Characterization of a subset of Cas9 orthologs using purified components reveals additional biochemical diversity, including both narrow and broad ranges of temperature dependence, staggered-end DNA target cleavage, and a requirement for long stretches of homology between gRNA and DNA target. Our results expand the available toolset of RNA-programmable CRISPR-associated nucleases.
Electron-phonon coupling induced intrinsic Floquet electronic structure
Authors: Song Zhigang , Wang Lin-Wang 
Published: November 2020

AbstractFloquet states are a topic of intense contemporary interest, which is often induced by coherent external oscillating perturbation (e.g., laser, or microwave) which breaks the continuous time translational symmetry of the systems. Usually, electron–phonon coupling modifies the electronic structure of a crystal as a non-coherent perturbation and seems difficult to form Floquet states. Surprisingly, we found that the thermal equilibrium electron–phonon coupling in M(MoS)3 and M(MoSe)3 (where M is a metallic element) exhibits a coherent behavior, and the electronic structure can be described by the Floquet theorem. Such a coherent Floquet state is caused by a selective giant electron–phonon coupling, with thermodynamic phonon oscillation serving as a driving force on the electronic part of the system. The quasi-1D Dirac cone at the Fermi energy has its band gap open and close regularly. Similarly, the electric current will oscillate even under a constant voltage.
Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication
Authors: Sun Xuepeng , Jiao Chen , Schwaninger Heidi , Chao C. Thomas , Ma Yumin , Duan Naibin , Khan Awais , Ban Seunghyun , Xu Kenong , Cheng Lailiang , Zhong Gan-Yuan , Fei Zhangjun 
Published: November 2020

AbstractDomestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domesticacv. Gala) and its two major wild progenitors,M. sieversiiandM. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality.
Harnessing the wisdom of crowds can improve guideline compliance of antibiotic prescribers and support antimicrobial stewardship
Authors: Krockow Eva M. , Kurvers R. H. J. M. , Herzog S. M. , Kämmer J. E. , Hamilton R. A. , Thilly N. , Macheda G. , Pulcini C. 
Published: November 2020

AbstractAntibiotic overprescribing is a global challenge contributing to rising levels of antibiotic resistance and mortality. We test a novel approach to antibiotic stewardship. Capitalising on the concept of “wisdom of crowds”, which states that a group’s collective judgement often outperforms the average individual, we test whether pooling treatment durations recommended by different prescribers can improve antibiotic prescribing. Using international survey data from 787 expert antibiotic prescribers, we run computer simulations to test the performance of the wisdom of crowds by comparing three data aggregation rules across different clinical cases and group sizes. We also identify patterns of prescribing bias in recommendations about antibiotic treatment durations to quantify current levels of overprescribing. Our results suggest that pooling the treatment recommendations (using the median) could improve guideline compliance in groups of three or more prescribers. Implications for antibiotic stewardship and the general improvement of medical decision making are discussed. Clinical applicability is likely to be greatest in the context of hospital ward rounds and larger, multidisciplinary team meetings, where complex patient cases are discussed and existing guidelines provide limited guidance.
Mitophagy-associated genes PINK1 and PARK2 are independent prognostic markers of survival in papillary renal cell carcinoma and associated with aggressive tumor behavior
Authors: Simon Adrian Georg , Tolkach Yuri , Esser Laura Kristin , Ellinger Jörg , Stöhr Christine , Ritter Manuel , Wach Sven , Taubert Helge , Stephan Carsten , Hartmann Arndt , Kristiansen Glen , Branchi Vittorio , Toma Marieta Ioana 
Published: November 2020

AbstractThe aim of this study was to investigate the mitophagy-related genes PINK1 and PARK2 in papillary renal cell carcinoma and their association with prognosis. In silico data of PINK1 and PARK2 were analyzed in TCGA cohorts of papillary renal cell carcinoma comprising 290 tumors and 33 corresponding non-neoplastic renal tissues. Protein expression data from a cohort of 95 papillary renal cell carcinoma patients were analyzed and associated with clinical-pathological parameters including survival. PINK1 and PARK2 were significantly downregulated in papillary renal cell carcinoma at transcript and protein levels. Reduced transcript levels of PINK1 and PARK2 were negatively associated with overall survival (p < 0.05). At the protein level, PARK2 and PINK1 expression were positively correlated (correlation coefficient 0.286, p = 0.04) and reduced PINK1 protein expression was prognostic for shorter survival. Lower PINK1 protein levels were found in tumors with metastases at presentation and in tumors of higher pT-stages. The multivariate analysis revealed mRNA expression of PINK1 and PARK2 as well as PINK1 protein expression as independent prognostic factors for shorter overall survival. The downregulation of PINK1 is a strong predictor of poor survival in papillary renal cell carcinoma. Immunohistochemical PINK1 expression in resected pRCC should be considered as an additional prognostic marker for routine practice.
Specifically bound BZIP transcription factors modulate DNA supercoiling transitions
Authors: Hörberg Johanna , Reymer Anna 
Published: November 2020

AbstractTorsional stress on DNA, introduced by molecular motors, constitutes an important regulatory mechanism of transcriptional control. Torsional stress can modulate specific binding of transcription factors to DNA and introduce local conformational changes that facilitate the opening of promoters and nucleosome remodelling. Using all-atom microsecond scale molecular dynamics simulations together with a torsional restraint that controls the total twist of a DNA fragment, we address the impact of torsional stress on DNA complexation with a human BZIP transcription factor, MafB. We gradually over- and underwind DNA alone and in complex with MafB by 0.5° per dinucleotide step, starting from the relaxed state to a maximum of 5° per dinucleotide step, monitoring the evolution of the protein-DNA contacts at different degrees of torsional strain. Our computations show that MafB changes the DNA sequence-specific response to torsional stress. The dinucleotide steps that are susceptible to absorbing most of the torsional stress become more torsionally rigid, as they are involved in protein-DNA contacts. Also, the protein undergoes substantial conformational changes to follow the stress-induced DNA deformation, but mostly maintains the specific contacts with DNA. This results in a significant asymmetric increase of free energy of DNA twisting transitions, relative to free DNA, where overtwisting is more energetically unfavourable. Our data suggest that specifically bound BZIP factors could act as torsional stress insulators, modulating the propagation of torsional stress along the chromatin fibre, which might promote cooperative binding of collaborative DNA-binding factors.
Cleavable hairpin beacon-enhanced fluorescence detection of nucleic acid isothermal amplification and smartphone-based readout
Authors: Ding Xiong , Yin Kun , Li Ziyue , Pandian Vikram , Smyth Joan A. , Helal Zeinab , Liu Changchun 
Published: November 2020

AbstractFluorescence detection of nucleic acid isothermal amplification utilizing energy-transfer-tagged oligonucleotide probes provides a highly sensitive and specific method for pathogen detection. However, currently available probes suffer from relatively weak fluorescence signals and are not suitable for simple, affordable smartphone-based detection at the point of care. Here, we present a cleavable hairpin beacon (CHB)-enhanced fluorescence detection for isothermal amplification assay. The CHB probe is a single fluorophore-tagged hairpin oligonucleotide with five continuous ribonucleotides which can be cleaved by the ribonuclease to specifically initiate DNA amplification and generate strong fluorescence signals. By coupling with loop-mediated isothermal amplification (LAMP), the CHB probe could detect Borrelia burgdorferi (B. burgdorferi) recA gene with a sensitivity of 100 copies within 25 min and generated stronger specific fluorescence signals which were easily read and analysed by our programmed smartphone. Also, this CHB-enhanced LAMP (CHB-LAMP) assay was successfully demonstrated to detect B. burgdorferi DNA extracted from tick species, showing comparable results to real-time PCR assay. In addition, our CHB probe was compatible with other isothermal amplifications, such as isothermal multiple-self-matching-initiated amplification (IMSA). Therefore, CHB-enhanced fluorescence detection is anticipated to facilitate the development of simple, sensitive smartphone-based point-of-care pathogen diagnostics in resource-limited settings.
Income is associated with hippocampal/amygdala and education with cingulate cortex grey matter volume
Authors: Lotze M. , Domin M. , Schmidt C. O. , Hosten N. , Grabe H. J. , Neumann N. 
Published: November 2020

AbstractIncome and education are both elements of a person’s socioeconomic status, which is predictive of a broad range of life outcomes. The brain’s gray matter volume (GMV) is influenced by socioeconomic status and mediators related to an unhealthy life style. We here investigated two independent general population samples comprising 2838 participants (all investigated with the same MRI-scanner) with regard to the association of indicators of the socioeconomic status and gray matter volume. Voxel-based morphometry without prior hypotheses revealed that years of education were positively associated with GMV in the anterior cingulate cortex and net-equivalent income with gray matter volume in the hippocampus/amygdala region. Analyses of possible mediators (alcohol, cigarettes, body mass index (BMI), stress) revealed that the relationship between income and GMV in the hippocampus/amygdala region was partly mediated by self-reported stressors, and the association of years of education with GMV in the anterior cingulate cortex by BMI. These results corrected for whole brain effects (and therefore not restricted to certain brain areas) do now offer possibilities for more detailed hypotheses-driven approaches.
Modelling the challenges of managing free-ranging dog populations
Authors: Belsare Aniruddha , Vanak Abi Tamim 
Published: November 2020

AbstractFree-ranging domestic dogs (FRD) are not only vectors of zoonoses of public health concern, but also pose direct threats to humans, livestock, and endangered wildlife. Many developing countries have struggled to control FRD, despite using both lethal and non-lethal methods. India has amongst the highest FRD populations globally and the highest incidences of dog-mediated human rabies, but only deploys Catch–Neuter–Vaccinate–Release (CNVR) for FRD control as a humane alternative to lethal methods, without evidence of it working successfully. Here, we use an agent-based dog population dynamics model to examine the time, effort, financial resources, and conditions needed to successfully control FRD in a typical urban setting. We simulate several scenarios, from an “ideal world” closed population with easily accessible dogs, to a more realistic open population with heterogeneity in catchability of dogs. In only one “best-case” scenario, CNVR resulted in a significant and lasting reduction in FRD, but with vaccination rates peaking only at 35%, which is half the WHO-recommended coverage. The customisable and portable modelling tool that we have developed allows managers to simulate real world processes and understand the expected effort needed to reduce regional dog populations, and assess methods for achieving effective anti-rabies vaccination coverage.
Super-resolution high-speed optical microscopy for fully automated readout of metallic nanoparticles and nanostructures
Authors: Alexandrov Andrey , Asada Takashi , De Lellis Giovanni , Di Crescenzo Antonia , Gentile Valerio , Naka Tatsuhiro , Tioukov Valeri , Umemoto Atsuhiro 
Published: November 2020

AbstractWe have designed a fully automated optical microscope running at high-speed and achieving a very high spatial resolution. In order to overcome the resolution limit of optical microscopes, it exploits the localized surface plasmon resonance phenomenon. The customized setup using a polarization analyzer, based on liquid crystals, produces no vibrations and it is capable of probing isolated nanoparticles. We tested its performance with an automated readout using a fine-grained nuclear emulsion sample exposed to 60 keV carbon ion beam and, for the first time, successfully reconstructed the directional information from ultra-short tracks produced by such low-energetic ions using a solid-state tracking detector.
Chronic heat stress regulates the relation between heat shock protein and immunity in broiler small intestine
Authors: Siddiqui Sharif Hasan , Kang Darae , Park Jinryong , Khan Mousumee , Shim Kwanseob 
Published: November 2020

AbstractChronic heat stress is considered to decrease the immune functions which makes negative effect on broiler growth performance. Here, we investigated the relationship between chronic heat stress, growth performance, and immunity in the small intestine of broilers. The study included two groups (control and heat stressed group) with eight replications per group. Ten broilers of 20-day aged were allocated in each replication. On day 35, the treatment group was subdivided into two groups based on their body weights (heavy and low body weight). Although, there was only the control and treatment group on day 28. The growth performance decreased and expression of heat shock protein 70 (HSP70), HSP60, and HSP47 increased on days 28 and 35 in the chronic heat stress group as compared with those in the control group. The expression levels of HSPs were significantly higher in the low body weight group than in the control group. The genes HSP70 and HSP60 were significantly associated with pro- and anti-inflammatory cytokines in the small intestine of the broilers of the treatment group. Thus, HSP70 and HSP60 activated the adaptive immunity in the small intestines of the broilers from the treatment group to allow adaptation to chronic heat stress environment.
Absorption cross section of gold nanoparticles based on NIR laser heating and thermodynamic calculations
Authors: Alrahili Mazen , Savchuk Viktoriia , McNear Kelly , Pinchuk Anatoliy 
Published: November 2020

AbstractWe present a method for measuring the optical absorption cross section ($$\sigma_{abs}$$

σ

abs

) of gold nanoparticles (GNPs) based on optically heating the solution of GNPs with an 808 nm near-infrared (NIR) laser and measuring the temperature increase of the solution. We rely on the theoretical calculations based on the heat diffusion equations and experimental measurements based on the energy balance equations to measure the $$\sigma_{abs}$$

σ

abs

and the temperature distribution of single GNPs. Several morphologies, including gold nanospheres (GNSs), spherical gold nanoparticle conjugate (AuNPC), which are 20 nm GNSs surface-functionalized with an IR 808 dye, gold nanorods (GNRs), and gold nanourchins (GNUs), were studied. The study found that a single 20 nm GNS has the lowest $$\sigma_{abs}$$

σ

abs

and temperature distribution as compared to 100 nm GNUs. By increasing the size of GNSs from 20 to 30 nm, the magnitude of $$\sigma_{abs}$$

σ

abs

as well as temperature distribution increases by a factor of 5. The $$\sigma_{abs}$$

σ

abs

values of 20 and 30 nm GNSs calculated by Mie theory and the experimentally measured are in a good agreement. GNRs with equivalent radius ($$R_{eq}$$

R

eq

) 9.16 nm show the second lowest $$\sigma_{abs}$$

σ

abs

. By increasing the $$R_{eq}$$

R

eq

by a factor of 2 to 19.2 nm, the measured $$\sigma_{abs}$$

σ

abs

and temperature distribution also increased by a factor of 2. We also estimated $$\sigma_{abs}$$

σ

abs

for GNUs with diameters at 80 and 100 nm, which also have higher $$\sigma_{abs}$$

σ

abs

values. This work confirms that we can use temperature to accurately measure the $$\sigma_{abs}$$

σ

abs

of a variety of GNPs in solution.
Light source optimization for partially coherent holographic displays with consideration of speckle contrast, resolution, and depth of field
Authors: Lee Seungjae , Kim Dongyeon , Nam Seung-Woo , Lee Byounghyo , Cho Jaebum , Lee Byoungho 
Published: November 2020

AbstractSpeckle reduction is an important topic in holographic displays as speckles not only reduce signal-to-noise ratio but also possess an eye-safety issue. Despite thorough exploration of speckle reduction methods using partially coherent light sources, the trade-off involved by the partial coherence has not been thoroughly discussed. Here, we introduce theoretical models that quantify the effects of partial coherence on the resolution and the speckle contrast. The theoretical models allow us to find an optimal light source that maximizes the speckle reduction while minimizing the decline of the other terms. We implement benchtop prototypes of partially coherent holographic displays using the optimal light source, and verify the theoretical models via simulation and experiment. We also present a criterion to evaluate the depth of field in partially coherent holographic displays. We conclude with a discussion about approximations and limitations inherent in the theoretical models.
Hybrid carbon thermal interface materials for thermoelectric generator devices
Authors: Chung Seok-Hwan , Kim Jong Tae , Kim Dong Hwan 
Published: November 2020

AbstractThermal interface materials (TIMs) are extensively used in electronic devices as efficient heat transfer materials. We fabricated all-carbon TIMs by hybridizing single-wall carbon nanotubes (SWCNTs) with graphite and demonstrated their performance by applying them to a thermoelectric generator (TEG) device. The hybrid carbon TIM exhibited maximum thermal conductivity when the SWCNT content was near 10 wt%. The TIM thermal contact resistance measured by a home-made calorimeter setup was 2.19 × 10−4 m2K/W, which did not vary with temperature but decreased with applied pressure. Post-treatment of the TIM with a silane coupling agent further reduced the TIM thermal contact resistance by 30%. When the TIM was placed between a TEG device and a copper heat reservoir, the TEG output power increased with the temperature difference across the TEG and applied pressure. Moreover, the post-treatment of the TIM enhanced the output power of the TEG device by up to 18.5%. This work provides a simple and effective pathway towards a carbon-based TIM that can be applied to a high temperature TEG.
Heavy Metal contamination of Dietary Supplements products available in the UAE markets and the associated risk
Authors: Jairoun Ammar Abdulrahman , Shahwan Moyad , Zyoud Sa’ed H. 
Published: November 2020

AbstractA specific safety concern is the possibility that a dietary supplement could be contaminated with heavy metals. This research was undertaken to investigate the daily exposure levels of heavy metals in dietary supplements available in the UAE and to explore the factors associated with the contamination of dietary supplements with heavy metals. A total of 277 dietary supplement samples were collected from the UAE market and prepared for the analysis of selected heavy metal contamination. Inductively coupled plasma mass spectrometry (ICP-MS) was used to determine the presence of heavy metals. The average daily intake of cadmium was 0.73 μg [95% CI 0.61–0.85], compared to the acceptable daily intake (ADI) of 6 μg; the daily intake of lead was 0.85 μg [95% CI 0.62–1.07], compared to the acceptable daily intake (ADI) of 20 μg; and the daily intake of arsenic was 0.67 μg [95% CI 0.57–0.78], compared to the acceptable daily intake of 10 μg. Although the dietary supplements available in the UAE have low levels of heavy metal contamination, numerous individuals are consuming a number of different dietary supplements every day and thereby may experience a cumulative level of toxic exposure. Dietary supplements formulations (Categories), dosage forms and country of origin are strong determents of heavy metal contamination in dietary supplements products.