bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical analysis on the effect of process parameters on deposition geometry in wire arc additive manufacturing
Authors: FAN Shilong , YANG Fei , ZHU Xiaonan , DIAO Zhaowei , CHEN Lin , RONG Mingzhe 
Published: January 2022

Abstract
Here we develop a two-dimensional numerical model of wire and arc additive manufacturing (WAAM) to determine the relationship between process parameters and deposition geometry, and to reveal the influence mechanism of process parameters on deposition geometry. From the predictive results, a higher wire feed rate matched with a higher current could generate a larger and hotter droplet, and thus transfer more thermal and kinetic energy into melt pool, which results in a wider and lower deposited layer with deeper penetration. Moreover, a higher preheat temperature could enlarge melt pool volume and thus enhance heat and mass convection along both axial and radial directions, which gives rise to a wider and higher deposited layer with deeper penetration. These findings offer theoretical guidelines for the acquirement of acceptable deposition shape and optimal deposition quality through adjusting process parameters in fabricating WAAM components.
Non-covalent interactions between molecular dimers (S66) in electric fields
Authors: Schwilk Max , Mezei Pál D , Tahchieva Diana N , von Lilienfeld O Anatole 
Published: January 2022

Abstract
Fine tuning and microscopic control of van der Waals interactions through oriented external electric fields (OEEFs) mandates an accurate and systematic understanding of intermolecular response properties. Having taken exploratory steps into this direction, we present a systematic study of interaction induced dipole electric properties of all molecular dimers in the S66 set, relying on CCSD(T)-F12b/aug-cc-pVDZ-F12 as reference level of theory. For field strengths up to ≈5 GV m−1 the interaction induced electric response beyond second order is found to be insignificant. Large interaction dipole moments (i.e. dipole moment changes due to van der Waals binding) are observed in the case of hydrogen bonding oriented along the intermolecular axis, and mostly small interaction dipole moments are found in dimers bonded by π-stacking or London dispersion. The interaction polarizabilities (i.e. polarizability changes due to van der Waals binding) were generally found to be small but always with a positive-valued principal component approximately aligned with the intermolecular axis, and two other negative-valued components. Energy decompositions according to symmetry adapted perturbation theory (SAPT0/jun-cc-pVDZ) suggest that electrostatics dominates the interaction dipole moment, with exchange and induction contributing on a smaller scale, and with dispersion having the smallest effect. First-order SAPT0 decomposition into monomer-resolved contributions enables us to establish a quantitative link between electric properties of monomers and dimers, which is found to be in qualitative agreement with the coupled cluster reference method. Using the aug-cc-pVQZ basis and non-empirical Perdew–Burke–Ernzerhof (PBE) semilocal exchange–correlation kernels, we also assess how density functional approximations in the nonlocal exchange and correlation parts affect the predictive accuracy: while dRPA@PBE0 based predictions are in excellent overall agreement with coupled cluster results, the computationally more affordable LC-ωPBE0-D3 level of theory also yields reliable results with relative errors below 5%. PBE alone, even when dispersion corrected, produces larger errors in interaction dipole moments (≈10%) and polarizabilities (≈20%). We also resolve the mutual impact of the three dimensions of the OEEF, and we present a discussion of the intermolecular distance dependence of the perturbations.
Persistent calyces increase floral longevity and female fitness inSalvia miltiorrhiza(Lamiaceae)
Authors: Li Deng-Fei , Yu Yan , Yang Hao-Jin , Yan Xian-Chun 
Published: January 2022

AbstractThe evolution of persistent calyces may be an adaptation to ensure reproductive success of certain flowering plants. However, experimental evidence of the functions of persistent calyces during flowering and seed development remains scarce. We explored the possible functions of persistent calyces in Salvia miltiorrhiza, a perennial herb with campanulate calyx. We conducted calyx manipulation experiments to examine whether persistent calyces affect visitation rates of nectar robbers and pollinators, individual flower longevity, fruit set, seed set and seed mass. Our findings suggested that shortening of the calyx significantly decreased individual flower longevity, fruit set and seed mass, but did not affect visitation of pollinators and nectar robbers. In addition, the seed set of control flowers and the flowers with calyx shortened at the beginning of fruiting stage (CSF flowers) did not significantly differ, but both were higher than that of the flowers with calyx shortened at the beginning of blooming stage (CSB flowers). The seed set and fruit set of CSB flowers were limited by pollination due to the reduction in floral longevity. We conclude that persistent calyces of S. miltiorrhiza may represent adaptive strategies to maintain floral longevity and increase plant fitness. Persistent calyces may provide protection for the growth of flowers and contribute resources to the development of fruits and seeds.
De-epithelialized Dermal Flap to Reduce Sacral Wound Healing Complications After Lower Body Lift Procedure
Authors: Zaussinger Maximilian , Wenny Raphael , Schwartz Bernhard , Ehebruster Gudrun , Huemer Georg M , Schmidt Manfred 
Published: January 2022

Abstract

Background
Lower or circumferential body lift procedures in the massive-weight-loss population have been associated with significant complication rates. Particularly, the sacral area is at risk of wound-healing problems due to high wound tension or shear forces.

Objectives
The authors introduced a de-epithelialized dermal flap to reinforce the sacral area.

Methods
Within this retrospective study, outcomes of 40 consecutive patients who underwent lower body lift between 2017 and 2021 were analyzed. The patient population was divided into 2 study groups (sacral flap vs no flap) including 20 patients each. Demographic and surgical data as well as complications were evaluated and compared. Appropriate statistical analysis was performed.

Results
Thirty-seven female and 3 male patients with a median age of 36.5 years (range, 23-54 years) and a mean weight loss of 46.3 ± 12 kg participated in the study. The most common complication was sacral wound dehiscence (n = 7, 17.5%), and its occurrence was statistically significantly lower in the sacral flap group (P = 0.037). The odd ratios for complications when executing the sacral flap procedure were reduced to 0.306 (95% confidence interval = 0.075 to 1.246) and 0.261 (95% confidence interval = 0.055 to 1.250) for the uncorrected and corrected logistic regressions, respectively. In addition, findings showed a significantly shorter hospital stay as well as statistical trends towards a lower occurrence of overall complications in the sacral flap group. Concerning the remaining data, no statistically significant differences between study groups were detected.

Conclusions
The presented de-epithelialized dermal flap leads to a significant reduction of sacral wound-healing complications and a shorter hospital stay for patients. This surgical technique is easily reproduceable, rapid, and effective; therefore, we would recommend it for each circumferential or lower body lift procedure.

Level of Evidence: 4
Heterogeneous cryo-EM projection image classification using a two-stage spectral clustering based on novel distance measures
Authors: Wang Xiangwen , Lu Yonggang , Lin Xianghong 
Published: January 2022

Abstract
Single-particle cryo-electron microscopy (cryo-EM) has become one of the mainstream technologies in the field of structural biology to determine the three-dimensional (3D) structures of biological macromolecules. Heterogeneous cryo-EM projection image classification is an effective way to discover conformational heterogeneity of biological macromolecules in different functional states. However, due to the low signal-to-noise ratio of the projection images, the classification of heterogeneous cryo-EM projection images is a very challenging task. In this paper, two novel distance measures between projection images integrating the reliability of common lines, pixel intensity and class averages are designed, and then a two-stage spectral clustering algorithm based on the two distance measures is proposed for heterogeneous cryo-EM projection image classification. In the first stage, the novel distance measure integrating common lines and pixel intensities of projection images is used to obtain preliminary classification results through spectral clustering. In the second stage, another novel distance measure integrating the first novel distance measure and class averages generated from each group of projection images is used to obtain the final classification results through spectral clustering. The proposed two-stage spectral clustering algorithm is applied on a simulated and a real cryo-EM dataset for heterogeneous reconstruction. Results show that the two novel distance measures can be used to improve the classification performance of spectral clustering, and using the proposed two-stage spectral clustering algorithm can achieve higher classification and reconstruction accuracy than using RELION and XMIPP.
Deep learning based on biologically interpretable genome representation predicts two types of human adaptation of SARS-CoV-2 variants
Authors: Li Jing , Wu Ya-Nan , Zhang Sen , Kang Xiao-Ping , Jiang Tao 
Published: January 2022

Abstract
Explosively emerging SARS-CoV-2 variants challenge current nomenclature schemes based on genetic diversity and biological significance. Genomic composition-based machine learning methods have recently performed well in identifying phenotype–genotype relationships. We introduced a framework involving dinucleotide (DNT) composition representation (DCR) to parse the general human adaptation of RNA viruses and applied a three-dimensional convolutional neural network (3D CNN) analysis to learn the human adaptation of other existing coronaviruses (CoVs) and predict the adaptation of SARS-CoV-2 variants of concern (VOCs). A markedly separable, linear DCR distribution was observed in two major genes—receptor-binding glycoprotein and RNA-dependent RNA polymerase (RdRp)—of six families of single-stranded (ssRNA) viruses. Additionally, there was a general host-specific distribution of both the spike proteins and RdRps of CoVs. The 3D CNN based on spike DCR predicted a dominant type II adaptation of most Beta, Delta and Omicron VOCs, with high transmissibility and low pathogenicity. Type I adaptation with opposite transmissibility and pathogenicity was predicted for SARS-CoV-2 Alpha VOCs (77%) and Kappa variants of interest (58%). The identified adaptive determinants included D1118H and A570D mutations and local DNTs. Thus, the 3D CNN model based on DCR features predicts SARS-CoV-2, a major type II human adaptation and is qualified to predict variant adaptation in real time, facilitating the risk-assessment of emerging SARS-CoV-2 variants and COVID-19 control.
PERCC1, a new member of theYap/TAZ/FAM181transcriptional co-regulator family
Authors: Sanchez-Pulido Luis , Jia Siyang , Hansen Carsten Gram , Ponting Chris P 
Published: January 2022

AbstractMotivationDisrupted PERCC1 gene expression causes an intractable congenital diarrhoea in infants. However, this gene’s molecular mechanism is unknown and no homologous proteins have been reported.ResultsOur detailed evolutionary analysis of PERCC1 sequence reveals it to be a previously unappreciated member of the YAP/TAZ/FAM181 family of homologous transcriptional regulators. Like YAP and TAZ, PERCC1 likely interacts with DNA via binding to TEA/ATTS domain transcription factors (TEADs) using its conserved interface-2 and -3 sequences. We compare the expression patterns of PERCC1 with those of YAP, TAZ, TEADs. Our report provides the identification and first in-depth bioinformatic analysis of a YAP/TAZ homologue, and a likely new regulator of the YAP/TAZ-TEAD transcriptional complex.Availability and implementationThe data underlying this article are available in UniProt Database.Supplementary informationSupplementary data are available at Bioinformatics Advances online.
SangeR: the high-throughput Sanger sequencing analysis pipeline
Authors: Schmid Kai , Dohmen Hildegard , Ritschel Nadja , Selignow Carmen , Zohner Jochen , Sehring Jannik , Acker Till , Amsel Daniel 
Published: January 2022

Abstract

Summary
In the era of next generation sequencing and beyond, the Sanger technique is still widely used for variant verification of inconclusive or ambiguous high-throughput sequencing results or as a low-cost molecular genetical analysis tool for single targets in many fields of study. Many analysis steps need time-consuming manual intervention. Therefore, we present here a pipeline-capable high-throughput solution with an optional Shiny web interface, that provides a binary mutation decision of hotspots together with plotted chromatograms including annotations via flat files.

Availability and implementation
SangeR is freely available at https://github.com/Neuropathology-Giessen/SangeR and https://hub.docker.com/repository/docker/kaischmid/sange_r

Contact
Kai.Schmid@patho.med.uni-giessen.de or Daniel.Amsel@patho.med.uni-giessen.de

Supplementary information
Supplementary data are available at Bioinformatics online.
A mixture model for determining SARS-Cov-2 variant composition in pooled samples
Authors: Valieris Renan , Drummond Rodrigo D , Defelicibus Alexandre , Dias-Neto Emmanuel , Rosales Rafael A , Tojal da Silva Israel 
Published: January 2022

AbstractMotivationDespite of the fast development of highly effective vaccines to control the current COVID–19 pandemics, the unequal distribution and availability of these vaccines worldwide and the number of people infected in the world lead to the continuous emergence of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) variants of concern. Therefore, it is likely that real-time genomic surveillance will be continuously needed as an unceasing monitoring tool, necessary to follow the spread of the disease and the evolution of the virus. In this context, new genomic variants of SARS-CoV-2, including variants refractory to current vaccines, makes genomic surveillance programs tools of utmost importance. Nevertheless, the lack of appropriate analytical tools to quickly and effectively access the viral composition in meta-transcriptomic sequencing data, including environmental surveillance, represent possible challenges that may impact the fast adoption of this approach to mitigate the spread and transmission of viruses.ResultsWe propose a statistical model for the estimation of the relative frequencies of SARS-CoV-2 variants in pooled samples. This model is built by considering a previously defined selection of genomic polymorphisms that characterize SARS-CoV-2 variants. The methods described here support both raw sequencing reads for polymorphisms-based markers calling and predefined markers in the variant call format. Results obtained using simulated data show that our method is quite effective in recovering the correct variant proportions. Further, results obtained by considering longitudinal data from wastewater samples of two locations in Switzerland agree well with those describing the epidemiological evolution of COVID-19 variants in clinical samples of these locations. Our results show that the described method can be a valuable tool for tracking the proportions of SARS-CoV-2 variants in complex mixtures such as waste water and environmental samples.Availability and implementationhttp://github.com/rvalieris/LCS.Supplementary informationSupplementary data are available at Bioinformatics online.
Optimizing nodal and staging classification in low rectal cancers with lateral node metastasis: multicentre retrospective cohort study
Authors: Shinto Eiji , Ike Hideyuki , Ito Masaaki , Takahashi Keiichi , Ohue Masayuki , Kanemitsu Yukihide , Suto Takeshi , Kinugasa Tetsushi , Watanabe Jun , Hida Jin-ichi , Itabashi Michio , Ozawa Heita , Nozawa Hiroaki , Kobayashi Hirotoshi , Hashiguchi Yojiro , Hase Kazuo , Sugihara Kenichi 
Published: January 2022

Abstract

Background
Patients with lateral node metastasis in low rectal cancers have a poor prognosis. However, variability in patient survival in terms of lateral metastatic status has not been thoroughly investigated. This study was conducted to assess the prognostic value of lateral node involvement and to review nodal classification.

Methods
Patients with stage III low rectal cancers who underwent lateral node dissection were retrospectively reviewed. Two cohorts were set: the first one (1995–2006) was selected using a Japanese multi-institutional database and was used for development of a new nodal system, and the second (2007–2013) was collected from referral institutions for validation of findings. Variables correlated with poor prognosis were investigated. Next, a modified classification of lateral-positive nodal cancers was created. Finally, this new classification was compared with TNM and Japanese classification-based systems according to the Akaike information criterion (AIC) and concordance index (c-index).

Results
Overall, 742 and 508 patients were selected for cohorts 1 and 2, respectively. Based on the analyses on cohort 1, patients with two or more lateral metastatic nodes partially spreading into regions outside of internal iliac area exhibited poor prognosis; accordingly, a modified N classification was created, where TNM-N1 and N2a cancers with this feature were upgraded, respectively, to N2a and N2b. The modified N classification yielded the most favourable indices (AIC = 2661.08; c-index = 0.6477) compared with the TNM (AIC = 2662.36; c-index = 0.6457) and Japanese classification-based systems (AIC = 2684.06; c-index = 0.6302). All findings were confirmed by analysing cohort 2.

Conclusion
A modified nodal system is proposed to account for the significance of lateral node metastasis.
Association between visit-to-visit blood pressure variability and risks of dementia in CKD patients: a nationwide observational cohort study
Authors: Park Sehoon , Cho Semin , Lee Soojin , Kim Yaerim , Park Sanghyun , Huh Hyeok , Kim Yong Chul , Han Seung Seok , Lee Hajeong , Lee Jung Pyo , Joo Kwon Wook , Lim Chun Soo , Kim Yon Su , Han Kyungdo , Kim Dong Ki 
Published: January 2022

ABSTRACTBackgroundThe association between visit-to-visit blood pressure (BP) variability and dementia risk in chronic kidney disease (CKD) patients has rarely been studied.MethodsIn this retrospective observational study, individuals who received three or more general health screenings were identified in the nationwide database of Korea. Those with persistent non-dialysis-dependent CKD [estimated glomerular filtration rate (eGFR) &lt;60 mL/min/1.73 m2 or dipstick albuminuria ≥1+] were included. The study exposure was systolic or diastolic BP variability, calculated as the variation independent of the mean and categorized into quartiles (Q4: the highest quartile; Q1: the lowest quartile). The risks of all-cause dementia, including Alzheimer's disease and vascular dementia, were analyzed by Cox regression adjusted for various clinical characteristics, including baseline BP and eGFR values.ResultsWe included 103 139 CKD patients and identified 7574 (7%) dementia events, including 5911 (6%) Alzheimer's disease cases, 886 (1%) vascular dementia events and 777 (1%) cases categorized as other types of dementia. Higher systolic BP variability was significantly associated with higher risks of all-cause dementia {[Q4 versus Q1], hazard ratio [HR] 1.173 [95% confidence interval (CI) 1.102–1.249], P for trend &lt; .001}. The results were also significant for the risk of Alzheimer's disease [HR 1.162 (95% CI 1.083–1.248), P &lt; .001] and vascular dementia [HR 1.282 (95% CI 1.064–1.545), P = .039]. The results were similar when diastolic BP variability was the exposure, as high diastolic BP variability was significantly associated with higher risks of all-cause dementia [HR 1.191 (95% CI 1.117,1.270), P &lt; .001].ConclusionsHigher visit-to-visit BP variability is significantly associated with a higher risk of dementia in CKD patients.
Outcomes and predictors of skin sodium concentration in dialysis patients
Authors: Salerno Fabio R , Akbari Alireza , Lemoine Sandrine , Filler Guido , Scholl Timothy J , McIntyre Christopher W 
Published: January 2022

ABSTRACT

Background
Sodium-23 magnetic resonance imaging (23Na MRI) allows the measurement of skin sodium concentration ([Na+]). In patients requiring dialysis, no data are available relating to the clinical outcomes associated with skin sodium accumulation or the determinants of increasing deposition.

Methods
This was an exploratory, observational study of adult hemodialysis (HD) and peritoneal dialysis (PD) patients. Participants underwent skin [Na+] quantification with leg 23Na MRI at the study’s beginning. Outcomes of interest were all-cause mortality and composite all-cause mortality plus major adverse cardiovascular events. Cumulative total and event-free survival were assessed using the Kaplan–Meier survival function after stratification into skin [Na+] quartiles. Cox proportional hazards regression was used to model the association between skin [Na+] and outcomes of interest. Multiple linear regression was used to model the predictors of skin [Na+].

Results
A total of 52 participants (42 HD and 10 PD) underwent the study procedures. The median follow-up was 529 days (interquartile range: 353–602). Increasing skin [Na+] quartiles were associated with significantly shorter overall and event-free survival (log-rank χ2(1) = 3.926, log-rank χ2(1) = 5.685; P for trend &lt;0.05 in both instances). Skin [Na+] was associated with all-cause mortality {hazard ratio (HR) 4.013, [95% confidence interval (95% CI) 1.988–8.101]; P &lt; 0.001} and composite events [HR 2.332 (95% CI 1.378–3.945); P &lt; 0.01], independently of age, sex, serum [Na+] and albumin. In multiple regression models, dialysate [Na+], serum albumin and congestive heart failure were significantly associated with skin [Na+] in HD patients (R2adj = 0.62).

Conclusions
Higher skin [Na+] was associated with worse clinical outcomes in dialysis patients and may represent a direct therapeutic target.