bluuebunny/crossref_metadata_2025_split huggingface dataset:
Restoration of evanescent waves in lens obeys Cesáro convergence
Authors: Nellambakam Yuganand , Chaitanya K V S Shiv 
Published: January 2021

Abstract
In this paper, we show that the restoration of the evanescent wave in a perfect lens obeys a new kind of convergence known as Cesàro convergence. Cesàro convergence allows us to extend the domain of convergence to the complex plane in terms of the Riemann zeta function. Therefore, from the Riemann zeta function properties, we show that it is not possible to restore the evanescent wave for all the values of reflection

r

z

′

, [here

r

z

′

is complex]. The special value, that is,

r

z

′

= 1/2 + ib refers to the non-existence of evanescent wave, is the physicist’s proof of the Riemann Hypothesis.
Complementary local-global approach for phonon mode connectivities
Authors: Gan Chee Kwan , Ong Zhun-Yong 
Published: January 2021

Abstract
Sorting and assigning phonon branches (e.g., longitudinal acoustic) of phonon modes is important for characterizing the phonon bands of a crystal and the determination of phonon properties such as the Grüneisan parameter and group velocity. To do this, the phonon band indices (including the longitudinal and transverse acoustic) have to be assigned correctly to all phonon modes across a path or paths in the Brillouin zone. As our solution to this challenging problem, we propose a computationally efficient and robust two-stage hybrid method that combines two approaches with their own merits. The first is the perturbative approach in which we connect the modes using degenerate perturbation theory. In the second approach, we use numerical fitting based on least-squares fits to circumvent local connectivity errors at or near exact degenerate modes. The method can be easily generalized to other condensed matter problems involving Hermitian matrix operators such as electronic bands in tight-binding Hamiltonians or in a standard density-functional calculation, and photonic bands in photonic crystals.
Classification of diffraction patterns in single particle imaging experiments performed at x-ray free-electron lasers using a convolutional neural network
Authors: Ignatenko Alexandr , Assalauova Dameli , Bobkov Sergey A , Gelisio Luca , Teslyuk Anton B , Ilyin Viacheslav A , Vartanyants Ivan A 
Published: January 2021

AbstractSingle particle imaging (SPI) is a promising method of native structure determination, which has undergone fast progress with the development of x-ray free-electron lasers. Large amounts of data are collected during SPI experiments, driving the need for automated data analysis. The necessary data analysis pipeline has a number of steps including binary object classification (single versus non-single hits). Classification and object detection are areas where deep neural networks currently outperform other approaches. In this work, we use the fast object detector networks YOLOv2 and YOLOv3. By exploiting transfer learning, a moderate amount of data is sufficient to train the neural network. We demonstrate here that a convolutional neural network can be successfully used to classify data from SPI experiments. We compare the results of classification for the two different networks, with different depth and architecture, by applying them to the same SPI data with different data representation. The best results are obtained for diffracted intensity represented by color images on a linear scale using YOLOv2 for classification. It shows an accuracy of about 95% with precision and recall of about 50% and 60%, respectively, in comparison to manual data classification.
Detection and impacts of tiling artifacts in MODIS burned area classification
Authors: Liu Tianjia , Crowley Morgan A 
Published: January 2021

Abstract
Since 2000, observations from the Moderate Resolution Imaging Spectroradiometer (MODIS) instrument, aboard the Terra and Aqua satellites, have been used to monitor global burned area and its trends. The FireCCI and MCD64A1 products classify burned area using algorithms that detect change in surface reflectance and separately process each ∼10° × 10° MODIS tile. We find that artifacts arise in both products from this tiling procedure. In particular, we find severe tiling artifacts in FireCCI, version 5.1 (FireCCI51) in northwest India and Pakistan, where the classified burned area is disjointed at the latitudinal boundary of two tiles that largely separates the Indian states of Punjab and Haryana. In contrast, this tiling effect is less noticeable in MCD64A1, Collection 6 (C6). As a result, while the average 2003–2019 October-November burned area in Haryana is of similar magnitude across the two products, that for Punjab is 13,381 km2 for MCD64A1 and just 1,486 km2 for FireCCI. We find moderate tiling artifacts in Southeast Asia and Eastern Europe. Our results highlight that additional processing is needed to ensure the continuity of burned area classification in FireCCI and MCD64A1, as well as other products relying on tile-dependent algorithms.
The Ethics and Aesthetics of Intertextual Writing: Cultural Appropriation and Minor Literature
Authors: Haynes Paul 
Published: January 2021

Abstract
Cultural appropriation, as both concept and practice, is a hugely controversial issue. It is of particular importance to the arts because creativity is often found at the intersection of cultural boundaries. Much of the popular discourse on cultural appropriation focusses on the commercial use of indigenous or marginalized cultures by mainstream or dominant cultures. There is, however, growing awareness that cultural appropriation is a complicated issue encompassing cultural exchange in all its forms. Creativity emerging from cultural interdependence is far from a reciprocal exchange. This insight indicates that ethical and political implications are at stake. Consequently, the arts are being examined with greater attention in order to assess these implications. This article will focus on appropriation in literature, and examine the way appropriative strategies are being used to resist dominant cultural standards. These strategies and their implications will be analyzed through the lens of Deleuze and Guattari’s notion of minor literature.
clinker & clustermap.js: automatic generation of gene cluster comparison figures
Authors: Gilchrist Cameron L M , Chooi Yit-Heng 
Published: January 2021

Abstract

Summary
Genes involved in biological pathways are often collocalised in gene clusters, the comparison of which can give valuable insights into their function and evolutionary history. However, comparison and visualization of gene cluster similarity is a tedious process, particularly when many clusters are being compared. Here, we present clinker, a Python based tool and clustermap.js, a companion JavaScript visualization library, which used together can automatically generate accurate, interactive, publication-quality gene cluster comparison figures directly from sequence files.

Availability and implementation
Source code and documentation for clinker and clustermap.js is available on GitHub (github.com/gamcil/clinker and github.com/gamcil/clustermap.js, respectively) under the MIT license. clinker can be installed directly from the Python Package Index via pip.

Supplementary information
Supplementary data are available at Bioinformatics online.
Codon usage pattern in Gnetales evolved in close accordance with the Gnetifer hypothesis
Authors: Majeed Aasim , Kaur Harpreet , Kaur Amitozdeep , Das Sreemoyee , Joseph Josepheena , Bhardwaj Pankaj 
Published: January 2021

AbstractThe evolution of Gnetales is ambiguous, and their phylogenetic position is still debated. The biological and molecular processes may evolve with the evolutionary history of a species or a clade. The molecular/biological processes of phylogenetically similar lineages closely follow their evolutionary pattern. If Gnetales evolved as a sister to Pinaceae, cupressophytes or Coniferales as a whole, then it is expected that the molecular or biological processes may reflect this pattern of evolution. In light of this, we deciphered the codon usage pattern of Gnetales, compared it with angiosperms, Pinaceae, cupressophytes and Coniferales as a whole. We evaluated whether this important molecular process has evolved in agreement with the Anthophyte, Gnepine, Gnecup or Gnetifer hypothesis. We observed that Gnetales prefer A/U-ending codons to G/C-ending codons like other lineages. Natural selection plays a dominant role in governing the codon usage bias (CUB). The CpA/CpT dinucleotides were over-represented, whereas the CpG dinucleotide was suppressed. Hierarchical clustering (HC) and correspondence analysis (CA) on relative synonymous codon usage values of 59 synonymous codons showed Gnetales as a sister clade to Coniferales as a whole and revealed that the codon usage pattern in Gnetales has evolved in close accordance with the Gnetifer hypothesis.
Two cortical representations of voice control are differentially involved in speech fluency
Authors: Neef Nicole E , Primaßin Annika , Gudenberg Alexander Wolff von , Dechent Peter , Riedel Christian , Paulus Walter , Sommer Martin 
Published: January 2021

Abstract
Recent studies have identified two distinct cortical representations of voice control in humans, the ventral and the dorsal laryngeal motor cortex. Strikingly, while persistent developmental stuttering has been linked to a white-matter deficit in the ventral laryngeal motor cortex, intensive fluency-shaping intervention modulated the functional connectivity of the dorsal laryngeal motor cortical network. Currently, it is unknown whether the underlying structural network organization of these two laryngeal representations is distinct or differently shaped by stuttering intervention. Using probabilistic diffusion tractography in 22 individuals who stutter and participated in a fluency shaping intervention, in 18 individuals who stutter and did not participate in the intervention and in 28 control participants, we here compare structural networks of the dorsal laryngeal motor cortex and the ventral laryngeal motor cortex and test intervention-related white-matter changes. We show (i) that all participants have weaker ventral laryngeal motor cortex connections compared to the dorsal laryngeal motor cortex network, regardless of speech fluency, (ii) connections of the ventral laryngeal motor cortex were stronger in fluent speakers, (iii) the connectivity profile of the ventral laryngeal motor cortex predicted stuttering severity (iv) but the ventral laryngeal motor cortex network is resistant to a fluency shaping intervention. Our findings substantiate a weaker structural organization of the ventral laryngeal motor cortical network in developmental stuttering and imply that assisted recovery supports neural compensation rather than normalization. Moreover, the resulting dissociation provides evidence for functionally segregated roles of the ventral laryngeal motor cortical and dorsal laryngeal motor cortical networks.
Exploiting common senses: sensory ecology meets wildlife conservation and management
Authors: Elmer Laura K , Madliger Christine L , Blumstein Daniel T , Elvidge Chris K , Fernández-Juricic Esteban , Horodysky Andrij Z , Johnson Nicholas S , McGuire Liam P , Swaisgood Ronald R , Cooke Steven J 
Published: January 2021

AbstractMultidisciplinary approaches to conservation and wildlife management are often effective in addressing complex, multi-factor problems. Emerging fields such as conservation physiology and conservation behaviour can provide innovative solutions and management strategies for target species and systems. Sensory ecology combines the study of ‘how animals acquire’ and process sensory stimuli from their environments, and the ecological and evolutionary significance of ‘how animals respond’ to this information. We review the benefits that sensory ecology can bring to wildlife conservation and management by discussing case studies across major taxa and sensory modalities. Conservation practices informed by a sensory ecology approach include the amelioration of sensory traps, control of invasive species, reduction of human–wildlife conflicts and relocation and establishment of new populations of endangered species. We illustrate that sensory ecology can facilitate the understanding of mechanistic ecological and physiological explanations underlying particular conservation issues and also can help develop innovative solutions to ameliorate conservation problems.
InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects
Authors: Chen X i , Mei Yang , Chen Mengyao , Jing Dong , He Yumin , Liu Feiling , He Kang , Li Fei 
Published: January 2021

Abstract
Sex determination and the regulation of sexual dimorphism are among the most fascinating topics in modern biology. As the most species-rich group of sexually reproducing organisms on Earth, insects have multiple sex determination systems. Though sex chromosomes and sex-biased genes are well-studied in dozens of insects, their gene sequences are scattered in various databases. Moreover, a shortage of annotation hinders the deep mining of these data. Here, we collected the chromosome-level sex chromosome data of 49 insect species, including 34 X chromosomes, 15 Z chromosomes, 5 W chromosomes and 2 Y chromosomes. We also obtained Y-linked contigs of four insects species—Anopheles gambiae, Drosophila innubila, Drosophila yakuba and Tribolium castaneum. The unannotated chromosome-level sex chromosomes were annotated using a standard pipeline, yielding a total of 123 030 protein-coding genes, 2 159 427 repeat sequences, 894 miRNAs, 1574 rRNAs, 5105 tRNAs, 395 snoRNAs (small nucleolar RNA), 54 snRNAs (small nuclear RNA) and 5959 other ncRNAs (non-coding RNA). In addition, 36 781 sex-biased genes were identified by analyzing 62 RNA-seq (RNA sequencing) datasets. Together with 5707 sex-biased genes from the Drosophila genus collected from the Sex-Associated Gene Database, we obtained a total of 42 488 sex-biased genes from 13 insect species. All these data were deposited into InSexBase, a new user-friendly database of insect sex chromosomes and sex-biased genes.
Database URL: http://www.insect-genome.com/Sexdb/.
Efficacy of Cover Crops for Pollinator Habitat Provision and Weed Suppression
Authors: Bryan Casey J , Sipes Sedonia D , Arduser Mike , Kassim Leila , Gibson David J , Scott Drew A , Gage Karla L 
Published: January 2021

AbstractPollinator declines have been documented globally, but little information is available about native bee ecology in Midwestern U.S. agriculture. This project seeks to optimize pollinator support and weed suppression in a 3-yr crop rotation with a fallow growing season. During fallow, one of five cover crop treatments (T1: crimson, red, and ladino clover and Bob oats [Fabales: Fabaceae - Trifolium incarnatum L., Trifolium pratense L., Trifolium repens L., and Cyperales: Poaceae - Avena sativa]; T2: crimson clover and oats; T3: red clover and oats; T4: ladino clover and oats; T5: no cover crop; T6/control: winter wheat [Cyperales: Poaceae - Triticum aestivum] L.) was seeded in one-half of 25 agricultural fields, whereas wheat was left unharvested in the other half as a comparison. Treatments that provide season-long floral resources support the greatest bee diversity and abundance (T1), and treatments with red clover support declining (Hymenoptera: Apidae) Bombus species (T1 and T3). Late-season floral resources may be important, yet limited (T1 and T4), and some species of agricultural weeds provide floral resources. Floral diversity may be less important than flower abundance or timing for pollinator diversity (T1–T4). Weed diversity was greatest in the no cover crop treatment (T5), least in winter wheat (T6), and intermediate in cover crop treatments (T1–T4) with no differences in weeds of economic concern. Wheat suppresses weeds but does not provide floral resources for pollinators. These results may also be applicable to marginal lands taken out of cultivation or field margin pollinator plantings in a typical corn–soybean rotation. Floral resource availability across the landscape is critical to maintain pollinator diversity.
Impact of left atrial strain mechanics on exercise intolerance and need for septal reduction therapy in hypertrophic cardiomyopathy
Authors: Saijo Yoshihito , Van Iterson Erik , Vega Brizneda Maria , Desai Milind Y , Lever Harry M , Smedira Nicholas G , Wierup Per , Thamilarasan Maran , Popović Zoran B , Grimm Richard A , Griffin Brian P , Xu Bo 
Published: January 2021

Abstract

Aims
We sought to assess the relationship between left atrial (LA) strain mechanics and exercise intolerance, and to evaluate the prognostic impact of LA strain mechanics on clinical deterioration necessitating septal reduction therapy in hypertrophic cardiomyopathy (HCM).

Methods and results
Consecutive HCM patients who underwent exercise stress echocardiography and cardiopulmonary exercise testing on the same day between October 2015 and April 2019 were enrolled prospectively. LA strain mechanics were analysed using speckle tracking echocardiography. LA stiffness was calculated as the ratio of E/e′ ratio to LA reservoir strain. The study cohort was divided into four groups based on the quartile of percent-predicted peak VO2, and exercise intolerance was defined as the lowest quartile (≤51%). Of 532 patients studied (mean age: 51 ± 15 years, 42% female), 138 patients demonstrated exercise intolerance. As exercise capacity worsened, LA strain mechanics worsened along a continuum (P &lt; 0.001). LA contractile strain with a cut-off of −13.9% was optimal at identifying exercise intolerance. On multivariable analysis, worse LA contractile strain was an independent predictor for exercise intolerance (P = 0.002). Of patients with left ventricular outflow tract obstruction, patients with LA stiffness worse than the median value (≥0.41) were significantly more likely to require septal reduction therapy than those with better LA stiffness (P = 0.026).

Conclusion
Worse LA contractile strain was an independent predictor for exercise intolerance in HCM. Patients with worse LA stiffness had a higher probability of clinical deterioration necessitating septal reduction therapy.
Endoscopic pancreatic duct stenting for pain palliation in selected pancreatic cancer patients: a systematic review and meta-analysis
Authors: Siddappa Pradeep K , Hawa Fadi , Prokop Larry J , Murad M Hassan , Abu Dayyeh Barham K , Chandrasekhara Vinay , Topazian Mark D , Bazerbachi Fateh 
Published: January 2021

Abstract

Background
Abdominal pain is a debilitating symptom affecting ∼80% of pancreatic cancer (PC) patients. Pancreatic duct (PD) decompression has been reported to alleviate this pain, although this practice has not been widely adopted. We aimed to evaluate the role, efficacy, and safety of endoscopic PD decompression for palliation of PC post-prandial obstructive-type pain.

Methods
A systematic review until 7 October 2020 was performed. Two independent reviewers selected studies, extracted data, and assessed the methodological quality.

Results
We identified 12 publications with a total of 192 patients with PC presenting with abdominal pain, in whom PD decompression was attempted, and was successful in 167 patients (mean age 62.5 years, 58.7% males). The use of plastic stents was reported in 159 patients (95.2%). All included studies reported partial or complete improvement in pain levels after PD stenting, with an improvement rate of 93% (95% confidence interval, 79%–100%). The mean duration of pain improvement was 94 ± 16 days. Endoscopic retrograde cholangiopancreatography (ERCP)-related adverse events (AEs) were post-sphincterotomy bleeding (1.8%), post-ERCP pancreatitis (0.6%), and hemosuccus pancreaticus (0.6%). AEs were not reported in two patients who underwent endoscopic ultrasound-guided PD decompression. In the 167 patients with technical success, the stent-migration and stent-occlusion rates were 3.6% and 3.0%, respectively. No AE-related mortality was reported. The methodological quality assessment showed the majority of the studies having low or unclear quality.

Conclusion
In this exploratory analysis, endoscopic PD drainage may be an effective and safe option in selected patients for the management of obstructive-type PC pain. However, a randomized–controlled trial is needed to delineate the role of this invasive practice.
Pervasive Mitonuclear Coadaptation Underlies Fast Development in Interpopulation Hybrids of a Marine Crustacean
Authors: Han Kin-Lan , Barreto Felipe S 
Published: January 2021

AbstractCellular energy production requires coordinated interactions between genetic components from the nuclear and mitochondrial genomes. This coordination results in coadaptation of interacting elements within populations. Interbreeding between divergent gene pools can disrupt coadapted loci and result in hybrid fitness breakdown. While specific incompatible loci have been detected in multiple eukaryotic taxa, the extent of the nuclear genome that is influenced by mitonuclear coadaptation is not clear in any species. Here, we used F2 hybrids between two divergent populations of the copepod Tigriopus californicus to examine mitonuclear coadaptation across the nuclear genome. Using developmental rate as a measure of fitness, we found that fast-developing copepods had higher ATP synthesis capacity than slow developers, suggesting variation in developmental rates is at least partly associated with mitochondrial dysfunction. Using Pool-seq, we detected strong biases for maternal alleles across 7 (of 12) chromosomes in both reciprocal crosses in high-fitness hybrids, whereas low-fitness hybrids showed shifts toward the paternal population. Comparison with previous results on a different hybrid cross revealed largely different patterns of strong mitonuclear coadaptation associated with developmental rate. Our findings suggest that functional coadaptation between interacting nuclear and mitochondrial components is reflected in strong polygenic effects on this life-history phenotype, and reveal that molecular coadaptation follows independent evolutionary trajectories among isolated populations.
A Draft Genome Assembly ofCulex pipiens pallens(Diptera: Culicidae) Using PacBio Sequencing
Authors: Peng Cheng , Qian Zhang , Xinyu Zhang , Qianqian Le , Maoqing Gong , Zhong Zhang , Ruiling Zhang 
Published: January 2021

AbstractThe Northern house mosquito, Culex pipiens pallens, serves as important temperate vectors of several diseases, particularly the epidemic encephalitis and lymphatic filariasis. Reference genome of the Cx. pipiens pallens is helpful to understand its genomic basis underlying the complexity of mosquito biology. Using 142 Gb (∼250×) of the PacBio long reads, we assembled a draft genome of 567.56 Mb. The assembly includes 1,714 contigs with a N50 length of 0.84 Mb and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 95.6% (n = 1,367). We masked 60.63% (344.11 Mb) of the genome as repetitive elements and identified 2,032 noncoding RNAs. A total of 18,122 protein-coding genes captured a 94.1% of BUSCO gene set. Gene family evolution and function enrichment analyses revealed that significantly expanded gene families mainly involved in immunity, gustatory and olfactory chemosensation, and DNA replication/repair.
ON SOME MODELS OF FERTILITY SELECTION
Authors: Feldman Marcus W , Christiansen Freddy B , Liberman Uri 
Published: January 2021

ABSTRACT
Additive, multiplicative and symmetric models of fertility controlled by one diallelic gene are studied. For the completely symmetric fertility system a complete equilibrium and local stability analysis is possible. Contrary to previous conjectures, asymmetric equilibria can be stable. Conditions are derived under which a multiplicative model can be regarded as equivalent to a symmetric fertility system.