bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cost-effective barcode system for maize genetic discrimination based on bi-allelic InDel markers
Authors: Liang Shuaiqiang , Lin Feng , Qian Yiliang , Zhang Tifu , Wu Yibo , Qi Yaocheng , Ren Sihai , Ruan Long , Zhao Han 
Published: July 2020

AbstractBackgroundMaize is one of the most important cereal crop all over the world with a complex genome of about 2.3 gigabase, and exhibits tremendous phenotypic and molecular diversity among different germplasms. Along with the phenotype identification, molecular markers have been accepted extensively as an alternative tool to discriminate different genotypes.ResultsBy using previous re-sequencing data of 205 lines, bi-allelic insertions and deletions (InDels) all over maize genome were screened, and a barcode system was constructed consisting of 37 bi-allelic insertion-deletion markers with high polymorphism information content (PIC) values, large discriminative size among varieties. The barcode system was measured and determined, different maize hybrids and inbreds were clearly discriminated efficiently with these markers, and hybrids responding parents were accurately determined. Compared with microarray data of more than 200 maize lines, the barcode system can discriminate maize varieties with 1.57% of different loci as a threshold. The barcode system can be used in standardized easy and quick operation with very low cost and minimum equipment requirements.ConclusionA barcode system was constructed for genetic discrimination of maize lines, including 37 InDel markers with high PIC values and user-friendly. The barcode system was measured and determined for efficient identification of maize lines.
Investigating the sequential patterns of methamphetamine use initiation in Iran
Authors: Sarani Ebrahim Moghimi , Ahmadi Jamshid , Oji Bahare , Mahi-Birjand Motahareh , Bagheri Nader , Bazrafshan Amir , Manshadi Marie Dehghan , Yaghoubi Sajad , Dezhkam Asiyeh , Khatami Mehrdad , Abdollahpour-Alitappeh Meghdad 
Published: July 2020

Abstract
Background
Methamphetamine (MA) remains one of the most commonly used amphetamine-type stimulants, accounting for the second most widely-used substance after marijuana. Due to increased use of MA, a wide variety of research has focused on the patterns of MA use initiation among adolescents. Nevertheless, there are few data available for people who use MA. The present study set out to assess the sequential patterns of substance use initiation in patients with MA use disorders in Iran.

Materials and methods
This cross-sectional study described substance initiation patterns for 302 patients who used MA admitted to hospitals and psychiatric centers of Shiraz University of Medical Sciences. The study was conducted between April 2015 and June 2016. After obtaining informed consents, participants were interviewed by trained interviewers using face-to-face, semi-structured interviews. The collecting data were analyzed using the chi square tests and one-way analysis of variance (ANOVA) tests to compare the relationship between qualitative and quantitative variables, respectively.

Results
Out of 302 participants enrolled in the study, 16 (5.3%) and 286 (94.7%) were female and male, respectively. The mean age of participants in the study was 37.29 years. The mean age of onset of MA use was found to be 15.9 years. 46.1% of the patients started MA use before 15 years. 77.2% of the patients who used MA had family members with a history of substance use. 93.71% of the patients who used MA started substance use with tobacco, alcohol, or opium, as the most frequent substances. Tobacco, as the first substance or starting substance, exhibited the most widely-used substance (69.53% of the cases). Tobacco-alcohol-cannabis-opium-heroin-MA sequencing was significantly related to the early onset of the substance use. Early-onset substance use was significantly higher in those with lower income, primary education, and family history of substance use. No significant relationship was found between employment status with the age of onset of substance use, and different substance use with marital status.

Conclusion
Tobacco, alcohol and opium can be considered as the main sequencing substances for initiation to MA use. Standardized measures to decrease and control access to main starting and sequencing substances, including tobacco, alcohol, and opium, can greatly help decrease the early onset of the MA use, develop suitable prevention, and establish early intervention strategies.
The effects of a prolonged exposure workshop with and without consultation on provider and patient outcomes: a randomized implementation trial
Authors: Foa Edna B. , McLean Carmen P. , Brown Lily A. , Zang Yinyin , Rosenfield David , Zandberg Laurie J. , Ealey Wayne , Hanson Brenda S. , Hunter Lora Rose , Lillard Ivett J. , Patterson Thomas J. , Rosado Julio , Scott Valerie , Weber Charles , Wise Joseph E. , Zamora Charles D. , Mintz Jim , Young-McCaughan Stacey , Peterson Alan L. ,   for the STRONG STAR Consortium
Published: July 2020

AbstractBackgroundProlonged exposure therapy (PE) is an evidence-based treatment for posttraumatic stress disorder (PTSD) that is underutilized in the military health system. Standard workshop training in PE may not be sufficient to alter provider behavior, but post-workshop consultation requires significant resources. Therefore, it is important to determine the incremental utility of post-workshop consultation.MethodsThis study used a hybrid type III randomized implementation trial at 3 US Army installations. Providers were randomized to receive a 4-day prolonged exposure workshop (Standard training condition,n= 60), or the prolonged exposure workshop followed by 6–8 months of post-workshop expert case consultation (Extended training condition,n= 43). The effects training condition were examined on provider attitudes (self-efficacy in delivering PE, expectations for patient improvement, and beliefs about PE), use of PE and PE components, and clinical outcomes of patients with PTSD (using the Clinician-Administered PTSD Scale (CAPS-5)).ResultsExtended condition providers reported greater improvements in self-efficacy,b= .83, 95% CI [.38, 1.27],t(79) = 3.71,p= .001, andd= .63. A greater proportion of patients in the Extended condition (44%) than in the Standard condition (27%) received at least 1 PE session,b= .76,t(233) = 2.53,p= .012, and OR = 2.13. Extended condition providers used more PE components (M= .9/session) than did Standard condition providers (M= .5/session),b= .54, 95% CI [.15, .93],t(68) = 2.70,p= .007, andd= .68. Finally, decrease in patients’ PTSD symptoms was faster for patients of Extended condition providers than for patients of Standard condition providers,b= − 1.81, 95% CI [− 3.57, − .04],t(263) = − 2.02,p= .045, andd= .66, and their symptoms were lower at the second assessment,b= − 5.47, 95% CI [− 9.30, − 1.63],t(210) = − 2.81,p= .005, andd= .66.ConclusionsPost-workshop consultation improved self-efficacy for delivering PE, greater use of PE, faster PTSD reduction, and lower PTSD severity at the second assessment. To our knowledge, this is the first demonstration that post-workshop case consultation for PE improves patient outcomes.Trial registrationClinicaltrials.gov,NCT02982538. Registered December 5, 2016; retrospectively registered
Pelvic bone marrow sparing intensity modulated radiotherapy reduces the incidence of the hematologic toxicity of patients with cervical cancer receiving concurrent chemoradiotherapy: a single-center prospective randomized controlled trial
Authors: Huang Jin , Gu Fei , Ji Tianlong , Zhao Jing , Li Guang 
Published: July 2020

Abstract
Purpose
To test the efficacy and feasibility of pelvic bone marrow sparing intensity modulated radiotherapy (PBMS-IMRT) in reducing grade 2 or higher hematological toxicity (HT2+) for patients with cervical cancer treated with concurrent chemoradiotherapy.

Methods and materials
A total of 164 patients with Stage Ib2–IIIb cervical cancer were prospectively enrolled from March 2018 to March 2019 at a single center and were randomly allocated into the PBMS group or the control group. The control group received weekly cisplatin concurrently with IMRT, followed by intracavitary brachytherapy. The PBMS group additionally received PBM dose constraint. The dosimetric parameters of the pelvic bone (PB) and the subsites including hip bone (HIP) and lumbosacral spine (LSS) and the corresponding bone marrow were recorded. The endpoint of the trial was acute hematologic or gastrointestinal toxicity. Receiver operating characteristic curves were used to derive optimal dosimetric planning constraints.

Results
Eighty-two patients in the PBMS group and 82 in the control group were enrolled for statistical analysis. The incidence of HT2+ in the PBMS group was 50.0%, significantly lower than the 69.5% incidence in the control group (P = 0.02). Patients with PB V40 ≥ 28% were more likely to experience HT2+ (OR = 2.85, P = 0.006), while the incidence of grade 2 or higher gastrointestinal toxicity (GT2+) events did not differ significantly between the two groups (P > 0.05). Dosimetric parameters of LSS showed stronger associations with HT2+ than other subsites. The patients with LSS V10 ≥ 87% and LSS mean ≥ 39 Gy were more likely to experience HT2+ (OR = 3.13, P = 0.001;OR = 3.03, P = 0.002, respectively).

Conclusion
PBMS-IMRT reduced HT compared with IMRT alone. Efforts to maintain LSS V10 < 87%, LSS mean < 39 Gy and PB V40 < 28% simultaneously may reduce the risk of HT2 +.

Trial registration
The trial was registered with Chinese clinical trial registry (ChiCTR1800015069).
Transcriptome network of the papillary thyroid carcinoma radiation marker CLIP2
Authors: Selmansberger Martin , Michna Agata , Braselmann Herbert , Höfig Ines , Schorpp Kenji , Weber Peter , Anastasov Natasa , Zitzelsberger Horst , Hess Julia , Unger Kristian 
Published: July 2020

Abstract
Background
We present a functional gene association network of the CLIP2 gene, generated by de-novo reconstruction from transcriptomic microarray data. CLIP2 was previously identified as a potential marker for radiation induced papillary thyroid carcinoma (PTC) of young patients in the aftermath of the Chernobyl reactor accident. Considering the rising thyroid cancer incidence rates in western societies, potentially related to medical radiation exposure, the functional characterization of CLIP2 is of relevance and contributes to the knowledge about radiation-induced thyroid malignancies.

Methods
We generated a transcriptomic mRNA expression data set from a CLIP2-perturbed thyroid cancer cell line (TPC-1) with induced CLIP2 mRNA overexpression and siRNA knockdown, respectively, followed by gene-association network reconstruction using the partial correlation-based approach GeneNet. Furthermore, we investigated different approaches for prioritizing differentially expressed genes for network reconstruction and compared the resulting networks with existing functional interaction networks from the Reactome, Biogrid and STRING databases. The derived CLIP2 interaction partners were validated on transcript and protein level.

Results
The best reconstructed network with regard to selection parameters contained a set of 20 genes in the 1st neighborhood of CLIP2 and suggests involvement of CLIP2 in the biological processes DNA repair/maintenance, chromosomal instability, promotion of proliferation and metastasis. Peptidylprolyl Isomerase Like 3 (PPIL3), previously identified as a potential direct interaction partner of CLIP2, was confirmed in this study by co-expression at the transcript and protein level.

Conclusion
In our study we present an optimized preselection approach for genes subjected to gene-association network reconstruction, which was applied to CLIP2 perturbation transcriptome data of a thyroid cancer cell culture model. Our data support the potential carcinogenic role of CLIP2 overexpression in radiation-induced PTC and further suggest potential interaction partners of the gene.
106Ruthenium eye plaque brachytherapy in the management of medium sized uveal melanoma
Authors: Jiang Ping , Purtskhvanidze Konstantine , Kandzia Gerit , Neumann Dirk , Luetzen Ulf , Siebert Frank-André , Roider Johann , Dunst Juergen 
Published: July 2020

Abstract
Background
To evaluate 106Ruthenium Brachytherapy in management of medium sized uveal melanoma, with emphasis on 5-year outcome and toxicity.

Methods
From April 2007 to October 2015, 39 patients with medium sized uveal melanoma were treated with 106 Ru eye plaques brachytherapy. At the time of diagnosis, the mean tumor depth was 3.7 mm (±SD:1.6 mm). The mean dose at the tumor apex was 141.4 Gy (± SD: 12.1 Gy) and 557.7 Gy (± SD: 257.3 Gy) to the sclera.

Results
Mean follow-up was 69.5 months (± SD: 53.8 months). Thirty-four patients (87.1%) remained free of recurrence. Twenty-six patients (66.7%) demonstrated a complete tumor regression after a median period of 12 months (3–60 mon.). By the final examination, the visual acuity of 26 patients (66.7%) was better than 20/200, and 12 patients (30.7%) had a visual acuity better than 20/40.
Retinopathy was detected in 11 patients (28.2%). After treatments only one patient (5.1%) had active vascular changes by the last examination. Moderate optic neuropathy was observed in 4 patients (10.3%). Cataract development was diagnosed in 21 patients (53.8%), and 16 patients (41%) had bilateral cataract development.
Special emphasis was made on patients with larger tumors. Twelve out of the 39 patients had a tumor with a depth of 5 mm or more. There was no significant difference in local control or in side effects between both groups observed.

Conclusions
Our study proved 106Ru -brachytherapy to be an excellent treatment option with regard to tumor control and preservation of the visual acuity in well-selected patients. Our data suggested that this treatment is also suitable for tumors with a depth of more than 5 mm.
Influence of transcatheter aortic valve replacement on patients with severe aortic stenosis undergoing non-cardiac surgery
Authors: Omoto Tadashi , Aoki Atsushi , Maruta Kazuto , Masuda Tomoaki , Horikawa Yui 
Published: July 2020

Abstract
Objectives
The purpose of this study was to clarify the influence of transcatheter aortic valve replacement (TAVR) in patients with aortic stenosis (AS) undergoing non-cardiac surgery.

Methods
Thirty-four patients with severe AS diagnosed by preoperative evaluation for non-cardiac surgery were reviewed and compared in two categories. First, patient profiles and surgical risk were compared before (pre-TAVR group; n = 10) and after (post-TAVR group; n = 24) the introduction of TAVR. Second, the completion rate of non-cardiac surgery and interval between the two cardiac and non-cardiac operations were compared between surgical aortic valve replacement (AVR) patients before the introduction of TAVR (pre-AVR group (n = 10)), in AVR patients after the introduction of TAVR (post-AVR (n = 12)), and in TAVR patients (TAVR group (n = 12)).

Results
Age and Japan score were higher in the post-TAVR group than in the pre-TAVR group. Malignancy was the most common non-cardiac disease (80%) in the pre-TAVR group, whereas orthopedic disease was the most common (50%) in the post-TAVR group. Completion rate of non-cardiac operation in the pre-AVR, post-AVR and TAVR groups was 70, 33, and 75% (post-AVR vs. TAVR: p = 0.010), and the interval between the two operations was 129 ± 98 days, 87 ± 40 days and 27 ± 15 days, respectively (pre AVR vs. TAVR: p = 0.034 and post AVR vs. TAVR: p = 0.025). In the post-TAVR group, AVR was selected because of a lack of fitness for TAVR in 5 of 12 patients.

Conclusions
After the introduction of TAVR, more senile and high-risk patients became candidates for a two-stage operation, and orthopedic conditions became the most common non-cardiac disease. Innovation in transcatheter valvular interventions and expansion of indications for patients currently evaluated as “unfit for TAVR” might be crucial issues for non-cardiac surgery with severe AS.
Bidirect effects from cisplatin combine with rosmarinic acid (RA) or hot water extracts of Glechoma hederacea (HWG) on renal cancer cells
Authors: Chou Su-Tze , Ho Bing-Ying , Tai Yu-Ting , Huang Chun-Jen , Chao Wen-Wan 
Published: July 2020

Abstract
Background
Cisplatin (CDDP) is a chemotherapeutic drug which also causes adverse side effects. Glechoma hederacea is a traditional Chinese herb belonging to the Labiatae family and has many biological activities. Our previous study indicated that rosmarinic acid (RA) was the most abundant phytochemical in G. hederacea. However, the antioxidant or anti-inflammatory effects of the combined treatment of G. hederacea, RA and CDDP on human renal cell carcinoma (RCC) 786-O cells have not been clearly demonstrated. We aimed to investigate the bioefficacy of hot water extracts of G. hederacea (HWG) and RA in inhibiting RCC 786-O cell activity and its synergism with CDDP against metastatic renal cancer cell.

Methods
Bioactivities of the combination treatment of HWG, RA, HWG/CDDP and RA/CDDP were assessed using the MTT assay and transwell migration, and the crude extract/compound efficacy was evaluated using wound healing migration assays, flow cytometry and western blotting.

Results
Our study indicates that CDDP inhibits 786-O cell proliferation and migration and HWG and RA protect against these effects. On the other hand, HWG and RA demonstrate a low cytotoxic effect in human renal proximal tubular epithelial cell line -2 (HK-2 cells). Cell cycle analysis found that HWG/CDDP and RA/CDDP combined treatment exerted cytotoxicity by inducing G2/M arrest and apoptosis. RA in combined with CDDP significantly inhibiting the expression of p-FAK (Tyr 925) in RCC 786-O cells in vitro.

Conclusion
We propose that the inhibition of RA on RCC 786-O cell invasion and migration may partly occur through the downregulation of FAK phosphorylation. The HWG/CDDP and RA/CDDP combined treatments may be effective strategies for intervention of RCC 786-O cell activity.
Experiences of caregivers of children with spinal muscular atrophy participating in the expanded access program for nusinersen: a longitudinal qualitative study
Authors: Kiefer Petra , Kirschner Janbernd , Pechmann Astrid , Langer Thorsten 
Published: July 2020

Abstract
Background
Expanded access programs (EAPs) allow patients with serious, life-threatening conditions access to drugs prior to their formal approval. Despite the possible benefits for patients, EAPs present several challenges, including uncertainty regarding a drug’s efficacy and safety as well as inequities regarding access to treatment. Although the number of EAPs is growing, the experience of patients participating in EAPs has not yet been studied. In Germany, an EAP for the treatment of Spinal Muscular Atrophy (SMA) with nusinersen ran from December 2016 to May 2017). SMA is a rare, progressive neuromuscular disorder characterized by muscle atrophy and proximal muscle weakness. Insights into patients’ and caregivers’ experiences could help to improve future EAPs.

Results
We conducted a prospective study using semi-structured interviews with caregivers of children with Spinal Muscular Atrophy (SMA) Type 1who participated in the nusinersen EAP in Germany. Interviews were transcribed verbatim and analyzed using an inductive approach according to the principles of content analysis. Eight families participated in the study. Their children were between 2 and 28 months old. Six children received non-invasive ventilation. Participation in the EAP marked an important turning point in the caregivers’ experiences. Their perspective changed from a severely limited life expectancy and a palliative approach to a more optimistic view including hopes for a longer life and positive development of their children. However, participating in the EAP was also challenging for caregivers in several ways. Lack of information regarding the launch of the program and the enrollment procedures caused significant uncertainty and stress among caregivers prior to the actual treatment. Further, concerns persisted that nusinersen could not be approved or that the child could be excluded due to an insufficient treatment response. Good communication and trusting relationships with medical and non-medical staff at the hospital helped caregivers cope with the uncertainties associated with the treatment.

Conclusion
From the caregivers’ perspective, there was no alternative to participating in the EAP for nusinersen. All participants were positive regarding their decision to participate. However, this study suggests that developing procedures to increase speed and transparency and to ensure fairness could help to further improve the system of EAPs as a way to provide urgently needed care to highly vulnerable patients.
The infantile neuroaxonal dystrophy rating scale (INAD-RS)
Authors: Atwal Paldeep S. , Midei Mark , Adams Darius , Fay Alexander , Heerinckx Frederic , Milner Peter 
Published: July 2020

Abstract
Background
INAD is an autosomal recessive neurogenetic disorder caused by biallelic pathogenic variants in PLA2G6. The downstream enzyme, iPLA2, plays a critical role in cell membrane homeostasis by helping to regulate levels of phospholipids. The clinical presentation occurs between 6 months and 3 years with global developmental regression, hypotonia, and progressive spastic tetraparesis. Progression is often rapid, resulting in severe spasticity, visual impairment, and cognitive decline, with many children not surviving past the first decade of life. To date, no accepted tool for assessing the severity of INAD exists; other commonly used scales (e.g. CHOP-INTEND, Modified Ashworth, Hammersmith Functional Motor Scale) do not accurately gauge the current severity of INAD, nor are they sensitive/specific enough to monitor disease progression. Finally, these other scales are not appropriate, because they do not address the combination of CNS, peripheral nerve, and visual pathology that occurs in children with INAD.

Methods
We have developed and validated a structured neurological examination for INAD (scored out of 80). The examination includes six main categories of pediatric developmental evaluation: 1) gross motor-and-truncal-stability skills, 2) fine motor skills, 3) bulbar function, 4) ocular function, 5) temporo-frontal function, and, 6) Functional evaluation of the autonomic nervous system. A cohort of patients diagnosed with INAD were followed prospectively to validate the score against disease severity and disease progression.

Results
We show significant correlation between the total neurological assessment score and months since symptom onset with a statistically significant (p = 6.7 × 10− 07) correlation between assessment score and disease onset. As hypothesized, the coefficient of months-since-symptom-onset is strongly negative, indicating a negative correlation between total score and months since symptom onset.

Conclusion
We have developed and validated a novel neurological assessment score in INAD that demonstrates strong correlation with disease severity and disease progression.