bluuebunny/crossref_metadata_2025_split huggingface dataset:
Virulence of Entomopathogenic Nematodes to Pupae ofFrankliniella fusca(Thysanoptera: Thripidae)
Authors: Gulzar Sehrish , Usman Muhammad , Wakil Waqas , Wu Shaohui , Oliveira-Hofman Camila , Srinivasan Rajagopalbabu , Toews Michael , Shapiro-Ilan David 
Published: June 2021

AbstractTobacco thrips, Frankliniella fusca (Hinds) is an economically significant pest. Entomopathogenic nematodes (EPNs) have shown promise as biocontrol agents against certain thrips species, but they have not been explored for suppression of F. fusca. We investigated the potential of EPNs to manage F. fusca by conducting three different bioassays: 1) a small cup dose–response bioassay (25, 50, and 100 IJs cm−2) with four EPN species, 2) a broad virulence bioassay with eight EPN species at 100 IJs cm−2, and 3) a potted soil bioassay testing with four EPN species (100 IJs cm−2). In the dose–response bioassay, all treatments showed relatively lower adult emergence when compared with the control group, but the minimum adult emergence (30%) was observed at 7 d post-treatment when Heterorhabditis bacteriophora (FL1-1) was applied at the highest rate (100 IJs cm−2). In the broad virulence study, all EPN treatments caused significant reductions in F. fusca adult emergence (18.3–75.0%) in comparison with the control. H. bacteriophora (Fl1-1) was more virulent than other nematode treatments but statistically not different from Steinernema feltiae and Steinernema riobrave, while Steinernema rarum was the least virulent. In the potted soil bioassay, the lowest emergence (10.6%) was observed in H. bacteriophora (Fl1-1) treatment, followed by S. feltiae (SN), S. riobrave (355), and Heterorhabditis indica (HOM1) treatments. These results indicate that EPNs have the ability to suppress the soil dwelling stage of F. fusca and should be explored further under greenhouse and field conditions for biocontrol potential within an integrated pest management (IPM) context.
Association Between Smoking and Molecular Subtypes of Colorectal Cancer
Authors: Wang Xiaoliang , Amitay Efrat , Harrison Tabitha A , Banbury Barbara L , Berndt Sonja I , Brenner Hermann , Buchanan Daniel D , Campbell Peter T , Cao Yin , Chan Andrew T , Chang-Claude Jenny , Gallinger Steven J , Giannakis Marios , Giles Graham G , Gunter Marc J , Hopper John L , Jenkins Mark A , Lin Yi , Moreno Victor , Nishihara Reiko , Newcomb Polly A , Ogino Shuji , Phipps Amanda I , Sakoda Lori C , Schoen Robert E , Slattery Martha L , Song Mingyang , Sun Wei , Thibodeau Steven N , Toland Amanda E , Van Guelpen Bethany , Woods Michael O , Hsu Li , Hoffmeister Michael , Peters Ulrike 
Published: June 2021

Abstract

Background
Smoking is associated with colorectal cancer (CRC) risk. Previous studies suggested this association may be restricted to certain molecular subtypes of CRC, but large-scale comprehensive analysis is lacking.

Methods
A total of 9789 CRC cases and 11 231 controls of European ancestry from 11 observational studies were included. We harmonized smoking variables across studies and derived sex study–specific quartiles of pack-years of smoking for analysis. Four somatic colorectal tumor markers were assessed individually and in combination, including BRAF mutation, KRAS mutation, CpG island methylator phenotype (CIMP), and microsatellite instability (MSI) status. A multinomial logistic regression analysis was used to assess the association between smoking and risk of CRC subtypes by molecular characteristics, adjusting for age, sex, and study. All statistical tests were 2-sided and adjusted for Bonferroni correction.

Results
Heavier smoking was associated with higher risk of CRC overall and stratified by individual markers (Ptrend &lt; .001). The associations differed statistically significantly between all molecular subtypes, which was the most statistically significant for CIMP and BRAF. Compared with never-smokers, smokers in the fourth quartile of pack-years had a 90% higher risk of CIMP-positive CRC (odds ratio = 1.90, 95% confidence interval = 1.60 to 2.26) but only 35% higher risk for CIMP-negative CRC (odds ratio = 1.35, 95% confidence interval = 1.22 to 1.49; Pdifference = 2.1 x 10-6). The association was also stronger in tumors that were CIMP positive, MSI high, or KRAS wild type when combined (Pdifference &lt; .001).

Conclusion
Smoking was associated with differential risk of CRC subtypes defined by molecular characteristics. Heavier smokers had particularly higher risk of CRC subtypes that were CIMP positive and MSI high in combination, suggesting that smoking may be involved in the development of colorectal tumors via the serrated pathway.
Experimental study on two consecutive droplets impacting onto an inclined solid surface
Authors: Chen Chun-Kuei , Chen Sheng-Qi , Yan Wei-Mon , Li Wen-Ken , Lin Ta-Hui 
Published: June 2021

Abstract
The present study is concerned with the experimental impingement of two consecutive droplets on an inclined solid surface. Attention is mainly paid to the effects of impingement timing with various oblique angles (Φ) of the surface on the impact phenomena, which mainly affect the maximum droplet spreading diameter. The investigation considers four impingement scenarios differentiated by impingement timing, namely Case 1: single-droplet impingement; Case 2 of Δt1: the moment when the leading droplet starts spreading along the oblique surface; Case 3 of Δt2: the moment when the leading droplet reaches its maximum spreading; and Case 4 of Δt3: the moment when the leading droplet starts retracting. It is observed that deformation behavior of two successive droplets impacting on the inclined surface experiences a complex asymmetric morphology evolution due to the enhancement of gravity effect and various conditions of the impingement timing. The merged droplet becomes slender with increasing oblique surface angle in the final steady shape, causing the decrease in the value of front and back contact angles. The impingement timing has a significant influence on the change of the maximum height of the merged droplet. The coalesced droplet spreads to the maximum dimensionless width diameter at Δt = Δt2 and the oblique angle of Φ = 45°, but reaches the maximum dimensionless height for Δt = Δt2 at Φ = 30°. The front contact angles converge to a fixed value eventually for all conditions of impingement timing, and the values become lower with the increasing surface inclination.
A fast semidiscrete optimal transport algorithm for a unique reconstruction of the early Universe
Authors: Levy Bruno , Mohayaee Roya , von Hausegger Sebastian 
Published: June 2021

ABSTRACT
We leverage powerful mathematical tools stemming from optimal transport theory and transform them into an efficient algorithm to reconstruct the fluctuations of the primordial density field, built on solving the Monge-Ampère-Kantorovich equation. Our algorithm computes the optimal transport between an initial uniform continuous density field, partitioned into Laguerre cells, and a final input set of discrete point masses, linking the early to the late Universe. While existing early universe reconstruction algorithms based on fully discrete combinatorial methods are limited to a few hundred thousand points, our algorithm scales up well beyond this limit, since it takes the form of a well-posed smooth convex optimization problem, solved using a Newton method. We run our algorithm on cosmological N-body simulations, from the AbacusCosmos suite, and reconstruct the initial positions of $\mathcal {O}(10^7)$ particles within a few hours with an off-the-shelf personal computer. We show that our method allows a unique, fast, and precise recovery of subtle features of the initial power spectrum, such as the baryonic acoustic oscillations.
Recombination machinery engineering facilitates metabolic engineering of the industrial yeast Pichia pastoris
Authors: Cai Peng , Duan Xingpeng , Wu Xiaoyan , Gao Linhui , Ye Min , Zhou Yongjin J 
Published: June 2021

Abstract
The industrial yeast Pichia pastoris has been harnessed extensively for production of proteins, and it is attracting attention as a chassis cell factory for production of chemicals. However, the lack of synthetic biology tools makes it challenging in rewiring P. pastoris metabolism. We here extensively engineered the recombination machinery by establishing a CRISPR-Cas9 based genome editing platform, which improved the homologous recombination (HR) efficiency by more than 54 times, in particular, enhanced the simultaneously assembly of multiple fragments by 13.5 times. We also found that the key HR-relating gene RAD52 of P. pastoris was largely repressed in compared to that of Saccharomyces cerevisiae. This gene editing system enabled efficient seamless gene disruption, genome integration and multiple gene assembly with positive rates of 68–90%. With this efficient genome editing platform, we characterized 46 potential genome integration sites and 18 promoters at different growth conditions. This library of neutral sites and promoters enabled two-factorial regulation of gene expression and metabolic pathways and resulted in a 30-fold range of fatty alcohol production (12.6–380 mg/l). The expanding genetic toolbox will facilitate extensive rewiring of P. pastoris for chemical production, and also shed light on engineering of other non-conventional yeasts.
The cooperative assembly of shelterin bridge provides a kinetic gateway that controls telomere length homeostasis
Authors: Liu Jinqiang , Hu Xichan , Bao Kehan , Kim Jin-Kwang , Zhang Catherine , Jia Songtao , Qiao Feng 
Published: June 2021

AbstractShelterin is a six-protein complex that coats chromosome ends to ensure their proper protection and maintenance. Similar to the human shelterin, fission yeast shelterin is composed of telomeric double- and single-stranded DNA-binding proteins, Taz1 and Pot1, respectively, bridged by Rap1, Poz1 and Tpz1. The assembly of the proteinaceous Tpz1-Poz1-Rap1 complex occurs cooperatively and disruption of this shelterin bridge leads to unregulated telomere elongation. However, how this biophysical property of bridge assembly is integrated into shelterin function is not known. Here, utilizing synthetic bridges with a range of binding properties, we find that synthetic shelterin bridge lacking cooperativity requires a linker pair that matches the native bridge in complex lifespan but has dramatically higher affinity. We find that cooperative assembly confers kinetic properties on the shelterin bridge allowing disassembly to function as a molecular timer, regulating the duration of the telomere open state, and consequently telomere lengthening to achieve a defined species-specific length range.
The ‘Ethical’ COVID-19 Vaccine is the One that Preserves Lives: Religious and Moral Beliefs on the COVID-19 Vaccine
Authors: Giubilini Alberto , Minerva Francesca , Schuklenk Udo , Savulescu Julian 
Published: June 2021

AbstractAlthough the COVID-19 pandemic is a serious public health and economic emergency, and although effective vaccines are the best weapon we have against it, there are groups and individuals who oppose certain kinds of vaccines because of personal moral or religious reasons. The most widely discussed case has been that of certain religious groups that oppose research on COVID-19 vaccines that use cell lines linked to abortions and that object to receiving those vaccine because of their moral opposition to abortion. However, moral opposition to COVID-19 vaccine research can be based on other considerations, both secular and religious. We argue that religious or personal moral objections to vaccine research are unethical and irresponsible, and in an important sense often irrational. They are unethical because of the risk of causing serious harm to other people for no valid reason; irresponsible because they run counter to individual and collective responsibilities to contribute to important public health goals; and in the case of certain kinds of religious opposition, they might be irrational because they are internally inconsistent. All in all, our argument translates into the rather uncontroversial claim that we should prioritize people’s lives over religious freedom in vaccine research and vaccination roll out.
HBI transcription factor-mediated ROS homeostasis regulates nitrate signal transduction
Authors: Chu Xiaoqian , Wang Jia-Gang , Li Mingzhe , Zhang Shujuan , Gao Yangyang , Fan Min , Han Chao , Xiang Fengning , Li Genying , Wang Yong , Yu Xiang , Xiang Cheng-Bin , Bai Ming-Yi 
Published: June 2021

Abstract
Nitrate is both an important nutrient and a critical signaling molecule that regulates plant metabolism, growth, and development. Although several components of the nitrate signaling pathway have been identified, the molecular mechanism of nitrate signaling remains unclear. Here, we showed that the growth-related transcription factors HOMOLOG OF BRASSINOSTEROID ENHANCED EXPRESSION2 INTERACTING WITH IBH1 (HBI1) and its three closest homologs (HBIs) positively regulate nitrate signaling in Arabidopsis thaliana. HBI1 is rapidly induced by nitrate through NLP6 and NLP7, which are master regulators of nitrate signaling. Mutations in HBIs result in the reduced effects of nitrate on plant growth and ∼22% nitrate-responsive genes no longer to be regulated by nitrate. HBIs increase the expression levels of a set of antioxidant genes to reduce the accumulation of reactive oxygen species (ROS) in plants. Nitrate treatment induces the nuclear localization of NLP7, whereas such promoting effects of nitrate are significantly impaired in the hbi-q and cat2 cat3 mutants, which accumulate high levels of H2O2. These results demonstrate that HBI-mediated ROS homeostasis regulates nitrate signal transduction through modulating the nucleocytoplasmic shuttling of NLP7. Overall, our findings reveal that nitrate treatment reduces the accumulation of H2O2, and H2O2 inhibits nitrate signaling, thereby forming a feedback regulatory loop to regulate plant growth and development.
The Conundrum of Kappa and Why Some Musculoskeletal Tests Appear Unreliable Despite High Agreement: A Comparison of Cohen Kappa and Gwet AC to Assess Observer Agreement When Using Nominal and Ordinal Data
Authors: Cibulka Michael T , Strube Michael J 
Published: June 2021

Abstract
In clinical practice, physical therapists often use different kinds of tests and measures in the assessment of their patients. For therapists to have confidence when using their tests and measures, an important attribute is having intratester and intertester reliability. Studies that assess reliability are cases of observer agreement. Many studies have been performed assessing observer agreement in the physical therapy literature. The most commonly used method to assess observer agreement studies that use nominal or ordinal data is the statistical method suggested by Cohen and the corresponding reliability coefficient, Cohen kappa. Recently, Cohen kappa has undergone scrutiny because of what is called kappa paradox, which occurs when observer agreement is high but the resulting kappa value is low. Another paradox also occurs when asymmetries exist between raters on their disagreements, resulting in a higher kappa value. In the physical therapy literature, there are numerous examples of this problem, which can often lead to misunderstanding the meaning of the data. This Perspective examines how and why these problems occur and suggests an alternative method for assessing observer agreement.
Business Restrictions and COVID-19 Fatalities
Authors: Spiegel Matthew , Tookes Heather 
Published: June 2021

AbstractWe collect a time-series database of business and related restrictions for every county in the United States from March through December 2020. We find strong evidence consistent with the idea that employee mask policies, mask mandates for the general population, restaurant and bar closures, gym closures, and high-risk business closures reduce future fatality growth. Other business restrictions, such as second-round closures of low- to medium-risk businesses and personal care/spa services, did not generate consistent evidence of lowered fatality growth and may have been counterproductive.
A New Pipeline for Removing Paralogs in Target Enrichment Data
Authors: Zhou Wenbin , Soghigian John , Xiang Qiu-Yun (Jenny) 
Published: June 2021

AbstractTarget enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely used pipelines for analysis of target enrichment data do not have a vigorous procedure to remove paralogs in target enrichment data. In this study, we develop a pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs from enrichment data. The new pipeline is an add-on to the existing HybPiper pipeline, and the entire pipeline applies criteria in both sequence similarity and heterozygous sites at each locus in the identification of paralogs. Users may adjust the thresholds of sequence identity and heterozygous sites to identify and remove paralogs according to the level of phylogenetic divergence of their group of interest. The new pipeline also removes highly polymorphic sites attributed to errors in sequence assembly and gappy regions in the alignment. We demonstrated the value of the new pipeline using empirical data generated from Hyb-Seq and the Angiosperms353 kit for two woody genera Castanea (Fagaceae, Fagales) and Hamamelis (Hamamelidaceae, Saxifragales). Comparisons of data sets showed that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed evident differences between data from HybPiper and data from our new PPD pipeline. We further evaluated the accuracy and error rates of PPD by BLAST mapping of putative paralogous and orthologous sequences to a reference genome sequence of Castanea mollissima. Compared to HybPiper alone, PPD identified substantially more paralogous gene sequences that mapped to multiple regions of the reference genome (31 genes for PPD compared with 4 genes for HybPiper alone). In conjunction with HybPiper, paralogous genes identified by both pipelines can be removed resulting in the construction of more robust orthologous gene data sets for phylogenomic and divergence time analyses. Our study demonstrates the value of Hyb-Seq with data derived from the Angiosperms353 probe set for elucidating species relationships within a genus, and argues for the importance of additional steps to filter paralogous genes and poorly aligned regions (e.g., as occur through assembly errors), such as our new PPD pipeline described in this study. [Angiosperms353; Castanea; divergence time; Hamamelis; Hyb-Seq, paralogs, phylogenomics.]
Force closure of the sacroiliac joint: cadaver study of the extent of gluteus maximus attachment on the sacrum and relative orientation of muscle fibers
Authors: Seim Sophia , Carey Fred , Andrews Ron , Jones Beth Moody 
Published: June 2021

The lumbosacral region has many muscles that may stabilize the region during functional activities via force closure (FC). The sacroiliac joint (SIJ) is a key element of this region. The role of individual muscles in FC of the SIJ is poorly understood. We undertook an anatomical study to examine the contribution of the gluteus maximus (GM) to FC.The posterior superior iliac spine (PSIS), sacrum, coccyx, and muscle fiber attachments of the GM were exposed on 30 embalmed cadavers. Sacral dimensions and specific GM muscle fiber attachment sites and their length were recorded. The angles of GM fibers relative to the SIJ were measured by goniometric technique at three specific points on the sacrum. All measurements were taken relative to a reference line connecting the most prominent point of the PSIS to the coccyx (line A).The mean width of GM attachment onto the sacrum at line A was 11.1 cm. At the midpoint of line A, GM extends past the SIJ attaching to the sacrum with a mean length of 3.13 cm and a mean angle of fiber alignment of 90 degrees. The orientation of GM fibers measured at the PSIS was 85.4 degrees.The GM's considerable length of attachment onto the sacrum and its angles of fiber alignment suggest that it may play a significant role in stabilization and force closure of the SIJ. Inclusion of GM recruitment and strengthening exercises may be beneficial for patients diagnosed with sacroiliac dysfunction.Grant Funding Source: none
Anatomical Variation in the Maximum Bending Moment of Metacarpals 2 through 5
Authors: Adar Tony , Baral Sumit , Hayes Westley , Saha Subrata , Pagano Anthony , Marquez Samuel 
Published: June 2021

Metacarpals (MC) two through five function as transmitters of force in activities involving the hand, making them susceptible to various types of fractures. An important clinical relevance is that the prevalence of metacarpal fractures has been estimated to be about 39% of all fractures of the hand. This study explores the relationship between maximum bending moment (MBM) and mid‐shaft diameter of embalmed cadaveric MC two through five in order to evaluate structural strength and fracture risk. Twelve donor bodies were examined followed by disarticulation and removal of all soft tissue of MC 2–5. All specimens were radiographed to assess for preexisting fractures and to rule out osteopenic changes. The samples were mechanically tested in three point bending using a Instron 8874 (Norwood, MA) Servohydraulic Test System. MBM was calculated for each MC and they ranged from 6.81 N·m to 3.60 N·m of MC2 to MC5 respectively. Our preliminary findings revealed a high positive correlation between mid‐shaft diameter and MBM (r2 = 0.96; p<0.05) suggesting that bending stresses resulting in MC fractures may be predicted with evaluation of mid‐shaft diameter, which may be of clinical importance.Grant Funding Source: SUNY Downstae College of Medicine
A suitable model to investigate the regeneration of transplanted hepatocytes
Authors: Itagaki Hiroko , Kitahara Shuji , Ezaki Taichi 
Published: June 2021

AimTo seek for a suitable site for isolated hepatocytes to proliferate with a high reliability, we established a mouse transplantation model and morphologically characterized the regeneration of transplanted ectopic hepatocytes.Materials & MethodsAdult male C57BL/6 mice were used as hepatocyte donors and hepatocytes were transplanted into mesenteric fat pads of C57BL/6‐Tg (CAG‐GFP) mice as recipients. At various times after transplantation of isolated hepatocytes (1.5×107 cells per site), mice were sacrificed and cryosections were made. Multiple‐immunostaining of various markers was employed for the 3‐dimentional imaging by the confocal laser‐scanning microscopy.Results & DiscussionThree weeks after transplantation, the transplanted hepatocytes vigorously regenerated to cell masses raging from 350μm to 2500μm in diameter. They are also acoompanied by the development of hepatic sinusoids of donor origin. The endotherial and type‐IV collagen linings of the sinusoids were comparable to those of the normal liver. Comparing with other transplantation sites, this model, therefore, provides a useful tool to investigate the regeneration of the liver structure and function after transplantation.