bluuebunny/crossref_metadata_2025_split huggingface dataset:
SmoothT—a server constructing low-energy pathways from conformational ensembles for interactive visualization and enhanced sampling
Authors: Staritzbichler René , Ristic Nikola , Stapke Tülin , Hildebrand Peter W 
Published: April 2023

Abstract

Motivation
The SmoothT software and webservice offers the construction of pathways from an ensemble of conformations. The user provides an archive of molecule conformations in Protein Databank (PDB) format, from which a starting and a final conformation need to be selected. The individual PDB files need to contain an energy value or score, estimating the quality of the respective confirmation. Additionally, the user has to provide a root-mean-square deviation (RMSD) cut-off, below which conformations are considered neighboring. From this, SmoothT constructs a graph that connects similar conformations.

Results
SmoothT returns the energetically most favorable pathway within in this graph. This pathway is directly displayed as interactive animation using the NGL viewer. Simultaneously, the energy along the pathway is plotted, highlighting the conformation that is currently displayed in the 3D window.

Availability and implementation
SmoothT is available as webservice at: http://proteinformatics.org/smoothT. Examples, a tutorial, and FAQs can be found there. Ensembles up to 2 GB (compressed) can be uploaded. Results will be stored for 5 days. The server is completely free and requires no registration. The C++ source code is available at: https://github.com/starbeachlab/smoothT.
The Responsibility Team—A Way to Ensure Children’s Right to Participation?
Authors: Sæbjørnsen Siv Elin Nord , Larsen Bjørn Kjetil , Ødegård Atle 
Published: April 2023

Abstract
Children’s effective participation seems to be difficult to achieve in practice. Although the United Nations Convention on the Rights of the Child came into force in 1989, recent research reports that effective participation rarely occurs. This qualitative study explores a group of adolescents’ views on participating in child welfare ‘responsibility teams’ (RTs) in Norway. The two specific foci are experiences regarding influence on their own situation and how the RT model may be a useful way to ensure children’s right to participate. The study concludes that RT alone cannot ensure children’s right to participate in the form of effective participation and that professional competencies are also important. The study calls for further research, especially on children and adolescents’ own experiences with RTs.
Impact of the RNA allosteric effect triggered by single nucleotide polymorphisms on the splicing process
Authors: Zhuang Youyuan , Lu Xiaoyan , Lin Peng , Wang Siyu , Sheng Xiaoran , Chen Chong , Zhang Guosi , Wang Zhiyi , Mei Changqiu , Qu Jia , Xu Liangde , Wang Hong 
Published: April 2023

Abstract
The susceptibility single nucleotide polymorphisms (SNPs) obtained by genome-wide association studies leave some thorny questions, such as prioritization, false positives and unknown pathogenesis. Previous studies suggested that genetic variation may perturb the RNA secondary structure, influence protein recruitment and binding and ultimately affect splicing processes. Therefore, exploring the perturbation of SNPs to structure–function correlations may provide an effective bridge toward understanding the genetic contribution to diseases. Here, aiming to decipher the regulatory mechanism of myopia susceptibility variants, we systematically evaluated the roles of SNP-induced structural changes during splicing. In addition, 7.53% of myopia-related SNPs exhibited significant global structural changes, 19.53% presented noteworthy local structural disturbance and there were wide-ranging structural perturbations in the splice-related motifs. We established a comprehensive evaluation system for structural disturbance in the splicing-related motifs and gave the priority ranking for the SNPs at RNA structural level. These high-priority SNPs were revealed to widely disturb the molecular interaction properties between splicing-related proteins and pre-mRNAs by HDOCK. Moreover, mini-gene assays confirmed that structural perturbation could influence splicing efficiency through structural remodelling. This study deepens our understanding of the potential molecular regulatory mechanisms of susceptible SNPs in myopia and contributes to personalized diagnosis, personalized medicine, disease-risk prediction and functional verification study by guiding the prioritization of the susceptibility SNPs.
Resistance is common in paediatric patients failing ART in South Africa
Authors: Hunt Gillian M , Yousif Mukhlid , Levin Leon , Ledwaba Johanna , Steegen Kim , Kufa Tendesayi , Zwane Hloniphile , Kalimashe Monalisa , Kana Vibha , Aynalem Getahun , Perlman Jaclyn , Ayalew Kassahun , Kindra Gurpreet , Diallo Karidia , Carmona Sergio , Sherman Gayle , Raizes Elliot J 
Published: April 2023

Abstract

Background
Minimal data exist on HIV drug resistance patterns and prevalence among paediatric patients failing ART in resource-limited settings. We assessed levels of HIV drug resistance in children with virological failure.

Methods
This cross-sectional study, performed from March 2017 to March 2019 in South Africa, enrolled HIV-positive children aged ≤19 years, receiving ART through public health facilities with recent evidence suggestive of virological failure (at least one viral load ≥1000 copies/mL), across 45 randomly selected high-volume clinics from all nine provinces. Resistance genotyping was performed using next-generation sequencing technologies. Descriptive analysis taking into account survey design was used to determine outcomes.

Results
Among 899 participants enrolled, the adjusted proportion of HIV drug resistance among children with virological failure was 87.5% (95% CI 83.0%–90.9%). Resistance to NNRTIs was detected in 77.4% (95% CI 72.5%–81.7%) of participants, and resistance to NRTIs in 69.5% (95% CI 62.9%–75.4%) of participants. Overall, resistance to PIs was detected in 7.7% (95% CI 4.4%–13.0%) of children.

Conclusions
HIV drug resistance was highly prevalent in paediatric patients failing ART in South Africa, with 9 in 10 patients harbouring resistance to NNRTIs and/or NRTIs. PI-based regimens are predicted to be highly efficacious in achieving virological suppression amongst patients failing NNRTI-based regimens. Scaling up resistance testing amongst patients would facilitate access to second- and third-line regimens in South Africa.
Diagnostic Performance of Anti-dsDNA Tests by Indirect Immunofluorescence and Enzyme-linked Immunosorbent Assay in Patients with Systemic Lupus Erythematosus
Authors: Nieto-Aristizábal Ivana , España Laura Jackeline , Ortega Jorge , Ruiz-Ordoñez Ingrid , Vivas Álvaro J , Castaño Gloria L , Castillo Carmen , Bautista-Vargas Mario , Suárez Ana , Cañas Carlos A , Tobón Gabriel J 
Published: April 2023

Abstract

Background
Several laboratory techniques for anti double-stranded (ds) DNA detection in systemic lupus erythematosus (SLE) are available, with variable diagnostic performance. We aimed to evaluate anti-dsDNA’s diagnostic performance by indirect immunofluorescence (IIF) and enzyme-linked immunosorbent assay (EIA).

Methods
We conducted a single-center retrospective (2015 to 2020) study. Patients with anti-dsDNA tests by IIF and EIA were included. We evaluated the indications, applications, concordance, positive predictive value (PPV) of anti-dsDNA to confirm SLE diagnosis or flares, and associations of disease manifestations with positivity with each technique.

Results
A total of 1368 reports of anti-dsDNA tests by IIF and EIA and the corresponding medical records of the patients were analyzed. The main indication for anti-dsDNA testing was to help in the diagnosis of SLE in 890 (65%) of the samples, and the main application after obtaining the results was SLE exclusion in 782 (57.2%) cases. The combination with the highest frequency was the negativity result by both techniques in 801 (58.5%) cases (Cohen kappa 0.57). Both methods were positive in 300 patients with SLE (Cohen kappa 0.42). The PPVs of anti-dsDNA tests to confirm diagnosis/flare was 79.64% (95% CI, 75.35–83.35) by EIA, 78.75% (95% CI, 74.27–82.62) by IIF, and 82% (95% CI, 77.26–85.93) when both were positive.

Conclusions
Anti-dsDNA detection by IIF and EIA are complementary and may indicate different clinical patterns in patients with SLE. The detection of anti-dsDNA antibodies by both techniques has a higher PPV than either separately for confirming SLE diagnosis or flares. These results highlight the need for evaluating both methods in clinical practice.
Enhancing three-dimensional convolutional neural network-based geometric feature recognition for adaptive additive manufacturing: a signed distance field data approach
Authors: Hilbig Arthur , Vogt Lucas , Holtzhausen Stefan , Paetzold Kristin 
Published: April 2023

Abstract
In the context of additive manufacturing, the adjustment of process data to individual geometric features offers the potential to further increase manufacturing speed and quality, while being widely underestimated in recent research. Unfortunately, the current non-uniform data handling in the CAD-CAM-Link results in a downstream data loss, that prevents the availability of geometric knowledge from being present at any time to apply the more advanced approaches of adaptive slicing and tool path generation. Automatic detection of various geometric entities would be beneficial for classifying partial surfaces and volumetric ranges to gain customized informational insights of geometric parameterization. In this work, an enhanced approach of geometric deep learning for the analysis of voxelized engineering parts will be presented to align the inference representations to modeling paradigms for complex design models like architected materials. Although the baseline voxel representation offers distinct advantages in detection accuracy, it comes with an adversely large memory footprint. The geometry discretization leads to high resolutions needed to capture various detail levels that prevent the analysis of fine-grained objects. To achieve efficient usage of three-dimensional (3D) deep learning techniques, we propose a 3D-convolutional neural network-based feature recognition approach using signed distance field data to limit the needed resolution. These implicit geometric data leverage the advantages of volumetric convolution while alleviating their disadvantages through the use of the continuous signed distance function. When analyzing computer-aided design data for geometric primitive features, a common application task in surface reconstruction of reverse engineering the proposed methodology, achieves a detection accuracy that is in line with the accuracy values achieved by comparable algorithms. This enables the recognition of fine-grained surface instances. The unambiguous shape information extracted could be used in subsequent adaptive slicing algorithms to achieve individual geometry-based hatch generation.
Venetoclax plus low-dose cytarabine in patients with newly diagnosed acute myeloid leukemia ineligible for intensive chemotherapy: an expanded access study in Japan
Authors: Asada Noboru , Ando Jun , Takada Satoru , Yoshida Chikashi , Usuki Kensuke , Shinagawa Atsushi , Ishizawa Kenichi , Miyamoto Toshihiro , Iida Hiroatsu , Dobashi Nobuaki , Okubo Sumiko , Honda Hideyuki , Soshin Tomomi , Nishimura Yasuko , Tsutsui Atsuko , Mukai Harumi , Yamamoto Kazuhito 
Published: April 2023

Abstract

Background
In a Phase 3 international clinical trial (VIALE-C), venetoclax plus low-dose cytarabine improved the response rate and overall survival versus placebo plus low-dose cytarabine in patients with newly diagnosed acute myeloid leukemia who were ineligible for intensive chemotherapy. After the enrollment period of VIALE-C ended, we conducted an expanded access study to provide preapproval access to venetoclax in combination with low-dose cytarabine in Japan.

Methods
Previously, untreated patients with acute myeloid leukemia who were ineligible for intensive chemotherapy were enrolled according to the VIALE-C criteria. Patients received venetoclax (600 mg, Days 1–28, 4-day ramp-up in Cycle 1) in 28-day cycles and low-dose cytarabine (20 mg/m2, Days 1–10). All patients took tumor lysis syndrome prophylactic agents and hydration. Safety endpoints were assessed.

Results
Fourteen patients were enrolled in this study. The median age was 77.5 years (range = 61–84), with 78.6% over 75 years old. The most common grade ≥ 3 treatment-emergent adverse event was neutropenia (57.1%). Febrile neutropenia was the most frequent serious adverse event (21.4%). One patient developed treatment-related acute kidney injury, leading to discontinuation of treatment. Two patients died because of cardiac failure and disease progression that were judged not related to study treatment. No patients developed tumor lysis syndrome.

Conclusions
The safety outcomes were similar to those in VIALE-C without new safety signals and were well managed with standard medical care. In clinical practice, more patients with severe background disease are expected, in comparison with in VIALE-C, suggesting that it is important to carefully manage and prevent adverse events.
Sources of Resistance, Effect of Maturity Groups, and Marker-Trait Associations Associated with Fusarium graminearum Causing Root Rot of Soybean (Glycine max)
Authors: Okello Paul , Solanki Shyam , Rafi Nitha , Mathew Febina M. 
Published: April 2023

Fusarium graminearum Schwabe is an important fungus causing root rot of soybean ( Glycine max L.) in the United States. In this study, 248 accessions (including the susceptible check ‘Williams 82’) from the United States Department of Agriculture germplasm collection (maturity group [MG] 0 to V) were screened with a single isolate of F. graminearum using the inoculum layer inoculation method in the greenhouse to identify resistant parental materials. Disease severity was evaluated 21 days postinoculation on a 1-to-5 rating scale and expressed as relative treatment effects (RTEs). Eight accessions (PI437949, PI438292, PI612761A, PI438094B, PI567301B, PI408309, PI361090, and P188788) had significantly lower RTEs when compared with Williams 82 based on 95% confidence intervals. Furthermore, the effect of MGs on disease severity was assessed, and accessions belonging to MG 0 or I had significantly greater RTEs than cultivars belonging to MGs II to V based on 95% confidence intervals. A genome-wide association study analysis was conducted using 42,079 single-nucleotide markers, and six marker-trait associations were identified that may be novel sources of F. graminearum resistance. The identification of new resistant parental materials and MTAs associated with resistance to F. graminearum will be useful in breeding programs for developing resistant cultivars. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Genome Sequencing of Strain Vm263, a Hypotoxic Strain of Valsa mali Causing Apple Valsa Canker
Authors: Li Dong-Shan , Guo Jia-Chen , Wang Ya-Nan , Hu Tong-Le , Cao Ke-Qiang , Wang Shu-Tong , Meng Xiang-Long 
Published: April 2023

Apple valsa canker, caused by Valsa mali, has seriously endangered the sustainable development of the apple industry in China. Our previous study revealed that low-temperature induction increased the pathogenicity of strain Vm263, which is a hypotoxic strain of V. mali causing apple valsa canker. However, the regulatory mechanism of this phenomenon was still unclear. In this study, whole genome sequencing of strain Vm263 was performed using a combination of long-read single-molecule real-time sequencing technology (Pacific Biosciences) and MGISEQ sequencing. The genome size of strain Vm263 was 42.83 Mb and the assembly N50 was 5.09 Mb. The genome provides a valuable resource for facilitating our understanding of the response of V. mali to low temperature. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
How Consistent are International Rotations Between Plastic Surgery Training Programs?
Authors: Reddy Narainsai K. , Sasson Daniel C. , Wester James R. , Gosain Arun K. 
Published: April 2023

Introduction:
Institutional partnerships between plastic surgery residency programs in the United States and providers in low- and middle-income countries can serve as bilateral and longitudinal capacity-building relationships. In the United States, obtaining approval for international rotations by a home institution and national review committee is highly encouraged but not required before resident international engagement. Acquiring approval at the institutional level is the first step to allow trainees to participate in international rotations on elective time rather than on vacation time. National approval through the American Council of Graduate Medical Education and American Board of Plastic Surgery allows cases to count toward the resident’s yearly case log.

Methods:
All 101 integrated and independent plastic surgery program directors/coordinators were asked to participate. The survey identified the requirements and details of existing international rotations.

Results:
In total, 57 programs responded (56% response rate) to the survey. An estimated 54% of all programs offered international rotations to their residents, and 94% of these programs obtained institutional approval. Additionally, 69% of these programs have received national approval.

Conclusions:
Institutional requirements for programs to provide international rotations vary significantly across institutions, which results in disparate experiences for residents and poses potential risks to international partners. This study will help promote transparency regarding international rotation requirements and better equip faculty to enhance international rotations that cater to the needs of the institution, residents, and most importantly, the host countries.
Acute effects of high-intensity resistance training on central blood pressure parameters of elderly hypertensive women: a crossover clinical trial
Authors: Galvão Luan , Póvoa Thaís Inácio Rolim , Jardim Paulo César Veiga , Lima Ana Luiza , Barroso Weimar Kunz Sebba , Seguro Camila Simões , Gentil Paulo , Jardim Thiago Veiga 
Published: April 2023

Objective:
Assess the acute effects of a high-intensity resistance training session on central blood pressure (CBP) parameters of elderly hypertensive women.

Methods:
Forty physically active hypertensive women were included in resistance training and control protocols. Resistance training exercises were bench press, leg press and lat pull-down. The resistance training protocol consisted of three sets of 10 repetitions to volitional failure with 90 s of rest between sets. No exercise was performed in the control protocol. CBP parameters were measured in four moments: before (PRE), immediately after (T0), 30 min (T30) and 60 min (T60) following both protocols.

Results:
Resistance training significantly increased central SBP (cSBP) 107.4 ± 16.3 vs. 117.5 ± 16.7), augmentation index ((24.9 ± 12.7 vs. 33.1 ± 12.0), pulse wave velocity (PWV 9.7 ± 1.0 vs. 10.3 ± 1.1), peripheral pulse pressure (pPP 48.5 ± 11.7 vs. 58.9 ± 13.1), central pulse pressure (cPP 38.3 ± 11.6 vs. 46.5 ± 13.1) and amplified pulse pressure (ampPP 10.2 ± 4.2 vs. 12.4 ± 5.6) immediately after exercises. The comparison between groups showed higher values of cSBP (117.5 ± 16.7 vs. 106.3 ± 14.6), augmentation index (20.9 ± 11.0 vs. 33.1 ± 12.0), pPP (46.6 ± 11.0 vs. 58.9 ± 13.1) and cPP (36 ± 10.2 vs. 46.5 ± 13.1) at T0. After 30 min, all variables returned to the baseline values.

Conclusion:
High-intensity resistance training session increased CBP parameters immediately after exercises, but those changes were not sustained after 30 min.
Impaired β2-adrenergic endothelium-dependent vasodilation in patients previously hospitalized with coronavirus disease 2019
Authors: Faconti Luca , Farukh Bushra , McNally Ryan J. , Brett Sally , Chowienczyk Phil J. 
Published: April 2023

Aim:
The pulse wave response to salbutamol (PWRS) – change in augmentation index (AIx) – provides a means to assess endothelial vasodilator function in vivo. Endothelial dysfunction plays a relevant role in the pathogenesis of hypertension and cardiovascular disease and appears to underlie many of the complications of coronavirus disease 2019 (COVID-19). However, to what degree this persists after recovery is unknown.

Methods:
Individuals previously hospitalized with COVID-19, those recovered from mild symptoms and seronegative controls with well known risk factors for endothelial dysfunction were studied. To assess the involvement of nitric oxide-cyclic guanosine monophosphate pathway (NO-cGMP) on PWRS, sildenafil was also administrated in a subsample.

Results:
One hundred and one participants (60 men) aged 47.8 ± 14.1 (mean ± SD) years of whom 33 were previously hospitalized with COVID-19 were recruited. Salbutamol had minimal effect on haemodynamics including blood pressure and heart rate. It reduced AIx in controls (n = 34) and those recovered from mild symptoms of COVID-19 (n = 34) but produced an increase in AIx in those previously hospitalized: mean change [95% confidence interval] −2.85 [−5.52, −0.188] %, −2.32 [−5.17,0.54] %, and 3.03 [0.06, 6.00] % for controls, those recovered from mild symptoms and those previously hospitalized, respectively (P = 0.001). In a sub-sample (n = 22), sildenafil enhanced PWRS (change in AIx 0.05 [−2.15,2.24] vs. −3.96 [−7.01. −2.18], P = 0.006) with no significant difference between hospitalized (n = 12) and nonhospitalized participants (n = 10).

Conclusions:
In patients previously hospitalized with COVID-19, there is long-lasting impairment of endothelial function as measured by the salbutamol-induced stimulation of the NO-cGMP pathway that may contribute to cardiovascular complications.

Graphical abstract:

http://links.lww.com/HJH/C164