bluuebunny/crossref_metadata_2025_split huggingface dataset:
A pipeline for complete characterization of complex germline rearrangements from long DNA reads
Authors: Mitsuhashi Satomi , Ohori Sachiko , Katoh Kazutaka , Frith Martin C. , Matsumoto Naomichi 
Published: July 2020

AbstractBackgroundMany genetic/genomic disorders are caused by genomic rearrangements. Standard methods can often characterize these variations only partly, e.g., copy number changes or breakpoints. It is important to fully understand the order and orientation of rearranged fragments, with precise breakpoints, to know the pathogenicity of the rearrangements.MethodsWe performed whole-genome-coverage nanopore sequencing of long DNA reads from four patients with chromosomal translocations. We identified rearrangements relative to a reference human genome, subtracted rearrangements shared by any of 33 control individuals, and determined the order and orientation of rearranged fragments, with our newly developed analysis pipeline.ResultsWe describe the full characterization of complex chromosomal rearrangements, by filtering out genomic rearrangements seen in controls without the same disease, reducing the number of loci per patient from a few thousand to a few dozen. Breakpoint detection was very accurate; we usually see ~ 0 ± 1 base difference from Sanger sequencing-confirmed breakpoints. For one patient with two reciprocal chromosomal translocations, we find that the translocation points have complex rearrangements of multiple DNA fragments involving 5 chromosomes, which we could order and orient by an automatic algorithm, thereby fully reconstructing the rearrangement. A rearrangement is more than the sum of its parts: some properties, such as sequence loss, can be inferred only after reconstructing the whole rearrangement. In this patient, the rearrangements were evidently caused by shattering of the chromosomes into multiple fragments, which rejoined in a different order and orientation with loss of some fragments.ConclusionsWe developed an effective analytic pipeline to find chromosomal aberration in congenital diseases by filtering benign changes, only from long read sequencing. Our algorithm for reconstruction of complex rearrangements is useful to interpret rearrangements with many breakpoints, e.g., chromothripsis. Our approach promises to fully characterize many congenital germline rearrangements, provided they do not involve poorly understood loci such as centromeric repeats.
Heavy metal remediation in soil with chemical amendments and its impact on activity of antioxidant enzymes in Lettuce (Lactuca sativa) and soil enzymes
Authors: Hong Young Kyu , Kim Jin Wook , Lee Sang Phil , Yang Jae E. , Kim Sung Chul 
Published: July 2020

AbstractChemical amendments have been used to remediate soils contaminated with heavy metals. However, there is little understanding on the impacts of these amendments on the physiological and biochemical functions of plants and soil. This study used in situ microcosm experiment to understand the effect of chemical amendments on antioxidant and soil enzyme activity in plant and soil with respect to heavy metal reduction. Three chemical amendments—acid mine drainage sludge (AMDS), limestone (LS), and steel slag (SS)—were applied to soil at 3, 5, and 10% mixing ratios, and lettuce (Lactuca sativa) was cultivated in that soil for 30 days. The results showed that bioavailable Cd and Pb in soil was reduced by 9.8–40.5% and 4.2–92.5%, respectively. The most efficient amendment for heavy metal reduction was AMDS. The uptake of Cd and Pb also decreased by 0.5–66.1 and 21.6–79.5%, respectively, depending on the amendment type and application ratio. The activity of three antioxidants—catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR)—was generally higher than the control with no amendments. This result indicated that there was minimal inhibition of antioxidant activity due to the reduction of heavy metal uptake. Also, no significant difference was observed in chemical amendments applied soil compared to control in terms of soil enzyme activity. However, correlation analysis between heavy metal concentration in soil and two soil enzyme activities showed that significantly negative correlation (p < 0.01) was observed between bioavailable Pb in soil and acid-phosphatase activity. This result might indicate that impact of bioavailable Pb was much higher than Cd in terms of inhibition of soil enzyme activity. Overall, the application of chemical amendments to heavy metal polluted had a positive effect on plant physiological function and soil enzyme activity with a reduction in bioavailable heavy metals in soil and plants.
Six new species of Begonia from Guangxi, China
Authors: Liu Yan , Tseng Yu-Hsin , Yang Hsun-An , Hu Ai-Qun , Xu Wei-Bin , Lin Che-Wei , Kono Yoshiko , Chang Chiung-Chih , Peng Ching-I , Chung Kuo-Fang 
Published: July 2020

Abstract
Background
With currently 1980 described species, the mega-diverse Begonia is now perhaps the 5th largest flowering plant genus, expanding rapidly from ca. 900 species in 1997 to its current size in merely two decades. In continuation of our studies of Asian Begonia, we report six additional new species from Guangxi, the region/province harboring the second richest Begonia flora of China.

Results
Based on morphological and molecular data, the new species B. aurora belongs to Begonia sect. Platycentrum, while the other five new species (viz. B. larvata, B. longiornithophylla, B. lui, B. scabrifolia, and B. zhuoyuniae) are members of Sect. Coelocentrum. Somatic chromosome numbers of B. longiornithophylla and B. zhuoyuniae at metaphase were counted as 2n = 30, consistent with previously reports for Sect. Coelocentrum.

Conclusions
With the addition of the six new species, the total number of Begonia species in Guangxi increases from 86 to 92. Detailed description, line drawings, and color plates are provided to aid in identification.
Utilising the nasal aperture for template stabilisation for guided surgery in the atrophic maxilla
Authors: Onclin Pieter , Kraeima Joep , Merema Bram B. J. , Meijer Henny J. A. , Vissink Arjan , Raghoebar Gerry M. 
Published: July 2020

Abstract
Background
Templates aim to facilitate implant placement in the prosthetically preferred position. Mucosa-supported and bone-supported templates are commonly used in the edentulous maxilla. In the atrophic maxilla (Cawood V and VI), however, these templates can be easily displaced due to a lack of supportive tissues, even in cases where anterior sites offer sufficient bone for implant placement. To assist in positioning and stabilisation, we designed a template that utilises the nasal aperture as a fulcrum to create a forced and exclusive fit. The aim of this study was to assess the clinical usability of the developed template and the corresponding implant placement accuracy in patients with edentulous atrophic maxillae. Deviations between planned and placed implant positions were measured by aligning pre- and post-operative cone beam computed tomography scans.

Results
Twenty-four implants were placed in 11 patients. One template did not fit properly due to a slight undercut. All implants could be placed with good primary stability. The implants had high accuracy at the implant shoulder (global deviation 1.1 ± 0.5 mm, lateral deviation 0.8 ± 0.5 mm) and a mean angular deviation of 7.2 ± 3.4°.

Conclusions
The developed surgical template offers stabilised and secure template placement in the edentulous atrophic maxilla, resulting in satisfying implant placement accuracy when using a semi-guided approach.

Trial registration
Netherlands Trial Register, NL6561, registered 26 September 2017.
Brief Montreal-Toulouse Language Assessment Battery: adaptation and content validity
Authors: Altmann Raira Fernanda , Ortiz Karin Zazo , Benfica Tainá Rossato , de Oliveira Eduarda Pinheiro , Pagliarin Karina Carlesso 
Published: July 2020

Abstract
Background
Evaluating patients in the acute phase of brain damage allows for the early detection of cognitive and linguistic impairments and the implementation of more effective interventions. However, few cross-cultural instruments are available for the bedside assessment of language abilities. The aim of this study was to develop a brief assessment instrument and evaluate its content validity.

Methods
Stimuli for the new assessment instrument were selected from the M1-Alpha and MTL-BR batteries (Stage 1). Sixty-five images were redesigned and analyzed by non-expert judges (Stage 2). This was followed by the analysis of expert judges (Stage 3), where nine speech pathologists with doctoral training and experience in aphasiology and/or linguistics evaluated the images, words, nonwords, and phrases for inclusion in the instrument. Two pilot studies (Stage 4) were then conducted in order to identify any remaining errors in the instrument and scoring instructions.

Results
Sixty of the 65 figures examined by the judges achieved inter-rater agreement rates of at least 80%. Modifications were suggested to 22 images, which were therefore reanalyzed by the judges, who reached high levels of inter-rater agreement (AC1 = 0.98 [CI = 0.96–1]). New types of stimuli such as nonwords and irregular words were also inserted in the Brief Battery and favorably evaluated by the expert judges. Optional tasks were also developed for specific diagnostic situations. After the correction of errors detected in Stage 4, the final version of the instrument was obtained.

Conclusion
This study confirmed the content validity of the Brief MTL-BR Battery. The method used in this investigation was effective and can be used in future studies to develop brief instruments based on preexisting assessment batteries.
Room for improvement in non-pharmacological systemic sclerosis care? — a cross-sectional online survey of 650 patients
Authors: Stöcker Juliane K. , Vonk Madelon C. , van den Hoogen Frank H. J. , Nijhuis-van der Sanden Maria W. G. , Spierings Julia , Staal J. Bart , Satink Ton , van den Ende Cornelia H. M. ,   on behalf of the ARCH study group
Published: July 2020

Abstract
Background/ objective
To gain insight in the use of current systemic sclerosis (SSc) care provided by health professionals from the patient perspective. We focused on referral reasons, treatment goals, the alignment with unmet care needs, and outcome satisfaction.

Methods
Dutch SSc patients from 13 participating rheumatology departments were invited to complete an online survey. Descriptive statistics were used to describe current use of non-pharmacological care and outcome satisfaction. Reasons for referral and treatment goals were encoded in International Classification of Function and Disability (ICF) terms.

Results
We included 650 patients (mean (standard deviation [SD]) age, 59.4 (11.4) years. 50% had contact with a health professional in the past year; 76.3% since disease onset. Physiotherapists were the most frequently visited in the past year (40.0%), followed by dental hygienists (11.4%) and podiatrists (9.2%). The three most common referral reasons were pain, joint mobility and cardiovascular functions. Fatigue, Raynaud’s phenomenon, physical limitations, reduced hand function and joint problems were mentioned by more than 25% of all respondents as unmet needs. The proportion of patients treated in the past year by a health professional who were satisfied with knowledge and expertise of their health professionals was 74.4%; 73% reported improved daily activities and better coping with complaints. However, 48.9% perceived that the collaboration between rheumatologist and health professional was never or only sometimes sufficient.

Conclusion
Despite the high outcome satisfaction and good accessibility of health professionals, there are obstacles in the access to non-pharmacological care and communication barriers between health professionals and rheumatologists.
Integrated single-molecule long-read sequencing and Illumina sequencing reveal the resistance mechanism of Psathyrostachys huashanica in response to barley yellow dwarf virus-GAV
Authors: Shen Chuan , Wei Caiyan , Li Jingyuan , Zhang Xudong , Wu Yunfeng 
Published: July 2020

AbstractAlthoughPsathyrostachys huashanicahas excellent potential for resistance gene mining and molecular genetic breeding, no reference genome is available. To date, most studies ofP. huashanicahave been focused on the creation of translocation lines and additional lines, as well as the development of molecular markers. Therefore, research at the transcriptional level is lacking. In this study, the full-length transcriptome ofP. huashanicawas sequenced using PacBio isoform sequencing (Iso-Seq) of a pooled RNA sample to explore the potential full-length transcript isoforms. We obtained 112,596 unique transcript isoforms with a total length of 114,957,868 base pairs (bp). Subsequently, Illumina sequencing reads were used to correct and trim the PacBio isoforms. We annotated 103,875 unigenes in at least one functional database, and identified a plethora of differentially-expressed genes (DEGs) that are involved in the defense responses ofP. huashanicaagainst barley yellow dwarf virus-GAV (BYDV-GAV). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these DEGs were mostly involved in plant-pathogen interaction, plant hormone signal transduction, and the mitogen-activated protein kinase (MAPK) signaling pathway. Additionally, we selected twenty of the RNA-seq identified resistance-related up-regulated genes, including MAPKs, cysteine-rich receptor-like protein kinases (CRPKs), calcium-dependent protein kinases (CDPKs), pathogenesis-related protein (PR) proteins, WRKYs, and disease resistance proteins, and validated their up-regulation in response to BYDV-GAV by quantitative real-time PCR. Our results indicate that a series of defense-related genes were induced inP. huashanicaduring BYDV-GAV infection. The full-length transcriptome dataset will contribute to improved use of stress-resistance genes ofP. huashanica, and serves as a reference database for the analysis of transcript expression inP. huashanica.
Mapping quantitative trait loci for disease resistance to false smut of rice
Authors: Han Yanqing , Li Deqiang , Yang Jun , Huang Fu , Sheng Hongyan , Sun Wenxian 
Published: July 2020

AbstractFalse smut of rice, an important emerging disease caused by Ustilaginoidea virens, greatly reduces grain yield and deteriorates grain quality in many rice-growing regions worldwide. Identification of quantitative trait loci (QTL) conferring false smut resistance will facilitate incorporation of false smut resistance into elite cultivars. In this study, a set of recombinant inbred lines (RILs) derived from a cross of a resistant rice landrace MR183–2 and a high susceptible line 08R2394 were evaluated to map resistance QTLs for false smut. A total of 179 simple sequence repeat (SSR) polymorphic markers were identified for constructing genetic linkage maps. Using a composite interval mapping method, five false smut resistance QTLs were detected on chromosomes 2, 4, 8 and 11 in the RIL population. Among these QTLs, qFsr8–1 within a small region on chromosome 8 represents a major quantitative locus explaining the greatest phenotypic variance. Gene annotation in this major QTL region provides a theoretical basis for cloning of resistance QTLs. The SSR markers genetically linked to qFsr8–1 are valuable for marker-assisted breeding for false smut resistance in rice. In addition, nine QTLs for heading date were detected in this population. Correlation analysis of disease resistance score and heading date indicates that false smut resistance negatively correlates with the growth period length in rice.
Provenance of upper Permian-lowermost Triassic sandstones, Wutonggou low-order cycle, Bogda Mountains, NW China: implications on the unroofing history of the Eastern North Tianshan Suture
Authors: Zheng Dong-Yu , Yang Wan 
Published: July 2020

AbstractThis study investigates the provenance of sedimentary rocks in Bogda Mountains, NW China, and reconstructs the lithology and unroofing history of the Eastern North Tianshan Suture. Petrographic point counting data of sandstones and compositions of conglomerates of upper Permian-lowermost Triassic Wutonggou low-order cycle from Zhaobishan, North Tarlong, Taodonggou, and Dalongkou sections in the southern and northern foothills of Bogda Mountains were used to interpret the temporal and spatial variations of lithology of the Eastern North Tianshan Suture, which is the sediment source area. Three compositional trends were identified. A trend of upward-increasing quartz content and granitic pebbles in Zhaobishan section suggests a change from the undissected volcanic arc, accretionary wedge and trench setting to predominantly transitional volcanic arc and subordinate accretionary wedge and trench, in the eastern part of the Eastern North Tianshan Suture. In North Tarlong and Taodonggou sections, however, the lithic content decreases and the contents of quartz and granitic pebbles increase up sections. These trends indicate that the western part of the Eastern North Tianshan Suture changed from an undissected volcanic arc to the transitional volcanic arc, accretionary wedge and trench. No clear trend in the lithic-rich sandstones of the Dalongkou section indicates that sediments were derived from the undissected volcanic arc in the Eastern North Tianshan Suture and local rift shoulders. Compositional variations of studied rocks suggest that the Eastern North Tianshan Suture was an amalgamated complex with great spatial and temporal heterogeneities in lithology and experienced persistent unroofing during late Permian-earliest Triassic. This study reconstructs a key element of the Chinese Tianshan Suture and serves as an example to understand the unroofing processes of ancient sutures.
Diagnostic and prognostic role of proton single-voxel spectroscopy (SVS) in non-lesional epilepsy pediatric patients: prospective controlled study
Authors: Faheem Mohamed H. , Dabour Ahmed S. , Abdelhaie Omima M. 
Published: July 2020

Abstract
Background
We aimed to verify the diagnostic and prognostic role of proton single-voxel spectroscopy (SVS) in children with non-lesional epilepsy and its add-on value to conventional MR. The prospective controlled study carried out on the epileptic patients who were regularly following in the pediatric neurology clinic in our university hospital, over the period from July 2017 to July 2018. It compared SVS findings (NAA/Cr, NAA/Cho, and NAA/Cho+Cr ratios) between the case (50 patients) and control group (20 children), between the cases with different seizures semiology and between the patients with intractable and non-intractable epilepsy.

Results
NAA/Cr ratio showed a significant difference between the patients with intractable and non-intractable epilepsy in the basal ganglia (P value 0.005) and white matter (P value 0.043) with cutoff values of 1.5 and 1.9 respectively. A significant difference of NAA/Cho ratio was found between generalized seizures cases and other seizures semiology in basal ganglia (P value 0.012) and cortex (P value <.001). There was no significant difference between the patient and control groups or between generalized seizures cases and the control group.

Conclusion
Proton SVS has limited diagnostic value in non-lesional epilepsy pediatric patients, in differentiation between generalized seizures and other seizure types, but, it has a good prognostic role in predicting patients who will develop intractable epilepsy.
Rituximab-CHOP With Early Rituximab Intensification for Diffuse Large B-Cell Lymphoma: A Randomized Phase III Trial of the HOVON and the Nordic Lymphoma Group (HOVON-84)
Authors: Lugtenburg Pieternella Johanna , de Nully Brown Peter , van der Holt Bronno , D’Amore Francesco A. , Koene Harry R. , de Jongh Eva , Fijnheer Rob , van Esser Joost W. , Böhmer Lara H. , Pruijt Johannes F. , Verhoef Gregor E. , Hoogendoorn Mels , Bilgin Memis Y. , Nijland Marcel , van der Burg-de Graauw Nicole C. , Oosterveld Margreet , Jie Kon-Siong G. , Larsen Thomas Stauffer , van der Poel Marjolein W. , Leijs Maria B. , Silbermann Matthijs H. , van Marwijk Kooy Marinus , Beeker Aart , Kersten Marie J. , Doorduijn Jeanette K. , Tick Lidwine W. , Brouwer Rolf E. , Lam King H. , Burggraaff Coreline N. , de Keizer Bart , Arens Anne I. , de Jong Daphne , Hoekstra Otto S. , Zijlstra-Baalbergen Josée M. 
Published: July 2020

PURPOSE Immunochemotherapy with rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) has become standard of care for patients with diffuse large B-cell lymphoma (DLBCL). This randomized trial assessed whether rituximab intensification during the first 4 cycles of R-CHOP could improve the outcome of these patients compared with standard R-CHOP. PATIENTS AND METHODS A total of 574 patients with DLBCL age 18 to 80 years were randomly assigned to induction therapy with 6 or 8 cycles of R-CHOP-14 with (RR-CHOP-14) or without (R-CHOP-14) intensification of rituximab in the first 4 cycles. The primary end point was complete remission (CR) on induction. Analyses were performed by intention to treat. RESULTS CR was achieved in 254 (89%) of 286 patients in the R-CHOP-14 arm and 249 (86%) of 288 patients in the RR-CHOP-14 arm (hazard ratio [HR], 0.82; 95% CI, 0.50 to 1.36; P = .44). After a median follow-up of 92 months (range, 1-131 months), 3-year failure-free survival was 74% (95% CI, 68% to 78%) in the R-CHOP-14 arm versus 69% (95% CI, 63% to 74%) in the RR-CHOP-14 arm (HR, 1.26; 95% CI, 0.98 to 1.61; P = .07). Progression-free survival at 3 years was 74% (95% CI, 69% to 79%) in the R-CHOP-14 arm versus 71% (95% CI, 66% to 76%) in the RR-CHOP-14 arm (HR, 1.20; 95% CI, 0.94 to 1.55; P = .15). Overall survival at 3 years was 81% (95% CI, 76% to 85%) in the R-CHOP-14 arm versus 76% (95% CI, 70% to 80%) in the RR-CHOP-14 arm (HR, 1.27; 95% CI, 0.97 to 1.67; P = .09). Patients between ages 66 and 80 years experienced significantly more toxicity during the first 4 cycles in the RR-CHOP-14 arm, especially neutropenia and infections. CONCLUSION Early rituximab intensification during R-CHOP-14 does not improve outcome in patients with untreated DLBCL.