bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity assessment and gene expression analysis of prolonged shelf-life genes in Mangalore melon (Cucumis melo ssp. agrestis var. acidulus)
Authors: Gunnaiah Raghavendra , Shet Ratnakar M. , Lamani Ashwini , Radhika Dattatraya H. , Jagadeesha Rudrappa C. 
Published: June 2021

Abstract
Mangalore melon (Cucumis melo ssp. agrestis var. acidulus) is a non-dessert melon, extensively grown in the coastal districts of South India, but hardly known to the rest of the World. Immature or mature fruits of Mangalore melon are used in preparation of delicious dishes such as vegetable stew, chutneys and curries. They are appreciated for nutritional values, long shelf life and biotic stress resistance. Seventy-nine accessions of Mangalore melon were collected from five states of South India and their genetic diversity was assessed using inter simple sequence repeat (ISSR) markers. Putative candidate genes of extended shelf life in Mangalore melon were studied by quantitative reverse transcription polymerase chain reaction in comparison with cantaloupe (Cucumis melo L.). Shelf life varied from 65 days to 300 days at room temperature. Six ISSR primers amplified 142 fragments ranging from 80 bp to 2380 bp with an average of 23.66 bands per marker on a high-resolution capillary electrophoresis system. Neighbor joining phylogenetic tree construction from the ISSR allele similarity based genetic distance revealed two major clusters with 46 and 33 accessions in each cluster. Expression of fruit ripening related genes of ethylene biosynthesis (1-aminocyclopropane-1-carboxylate synthase, 1-aminocyclopropane-1-carboxylate oxidase) and cell wall metabolism (polygalacturonase, xyloglucan endotransglucosylase/hydrolase and expansin) in Mangalore melons was significantly lower than the cantaloupe melon at 180 days after harvest. Mangalore melon is a promising genetic resource for enhancing the shelf life of melons and the putative candidate genes are useful in enhancing shelf life of cantaloupe following validation and conformation.
Wavefront aberrations induced from biomechanical effects after customized myopic laser refractive surgery in finite element model
Authors: Du Ruirui , Fang Lihua , Peng Weijian , Yang Ruizhi , Nie Shifeng , Xiao Huirong , Gong Jiahui , Dai Yu , Deng Jiahao 
Published: June 2021

Abstract
Purpose
A customized myopic refractive surgery was simulated by establishing a finite element model of the human eye,after which we studied the wavefront aberrations induced by biomechanical effects and ablation profile after wavefront-guided LASIK surgery.
Methods
Thirty myopia patients (i.e., 60 eyes) without other eye diseases were selected. Their ages, preoperative spherical equivalent, astigmatism, and wavefront aberration were then obtained, in addition to the mean spherical equivalent error range − 4 to -8D. Afterward, wavefront-guided customized LASIK surgery was simulated by establishing a finite element eye model, followed by the analysis of the wavefront aberrations induced by the surface displacement from corneal biomechanical effects, as well as customized ablation profile. Finally, the preoperative and induced aberrations were statistically analyzed.
Results
Comatic aberrations were the main wavefront abnormality induced by biomechanical effects, and the wavefront aberrations induced by the ablation profile mainly included coma and secondary-coma, as well as sphere and secondary-sphere aberrations. Overall, the total high-order aberrations (tHOAs), total coma (C31), and sphere () increased after wavefront-guided customized LASIK surgery. According to our correlation analyses, coma, sphere, and total high-order aberrations were significantly correlated with decentration. Additionally, the material parameters of ocular tissue were found to affect the postoperative wavefront aberrations. When the material parameters of the sclera remained constant but those of cornea increased, the induced wavefront aberrations were reduced.
Conclusion
All biomechanical effects of cornea and ablation profile had significant effects on postoperative wavefront aberrations after customized LASIK refractive surgery; however, the effects of the ablation profile were more notorious.Additionally,the characteristics of biomechanical materials have influence on the clinical correction effect.
Self-assembling Peptide Discovery: Overcoming Human Bias With Machine Learning
Authors: Batra Rohit , Loeffler Troy , Chan Henry , Sriniva Srilok , Cui Honggang , Korendovych Ivan , Nanda Vikas , Palmer Liam , Solomon Lee , Fry Harry , Sankaranarayanan Subramanian 
Published: June 2021

Abstract
Peptide materials have a wide array of functions from tissue engineering, surface coatings to catalysis and sensing. This class of biopolymer is composed of a sequence, comprised of 20 naturally occurring amino acids whose arrangement dictate the peptide functionality. While it is highly desirable to tailor the amino acid sequence, a small increase in their sequence length leads to dramatic increase in the possible candidates (e.g., from tripeptide = 20^3 or 8,000 peptides to a pentapeptide = 20^5 or 3.2 M). Traditionally, peptide design is guided by the use of structural propensity tables, hydrophobicity scales, or other desired properties and typically yields <10 peptides per study, barely scraping the surface of the search space. These approaches, driven by human expertise and intuition, are not easily scalable and are riddled with human bias. Here, we introduce a machine learning workflow that combines Monte Carlo tree search and random forest, with molecular dynamics simulations to develop a fully autonomous computational search engine (named, AI-expert) to discover peptide sequences with high potential for self-assembly (as a representative target functionality). We demonstrate the efficacy of the AI-expert to efficiently search large spaces of tripeptides and pentapeptides. Subsequent experiments on the proposed peptide sequences are performed to compare the predictability of the AI-expert with those of human experts. The AI performs on-par or better than human experts and suggests several non-intuitive sequences with high self-assembly propensity, outlining its potential to overcome human bias and accelerate peptide discovery.
Characterization of Primary Direct Acting Antiviral Drugs (DAA) Resistance Mutations in NS5A/NS5B Regions of Hepatitis C Virus with Genotype 1a and 1b from Patients with Chronic Hepatitis
Authors: Santos Ana Paula de Torres , Silva Vanessa Cristina Martins , Mendes-Corrêa Maria Cássia J , Lemos Marcilio Figueiredo , Malta Fernanda de Mello , Santana Rúbia Anita Ferraz , Dastoli Gregório Tadeu Fernando , de Castro Vanessa Fusco Duarte , Pinho João Renato Rebello , Moreira Regina Célia 
Published: June 2021

Abstract
Hepatitis C virus (HCV) infection is a public health problem with an estimated 71 million infected people worldwide. The high level of HCV replication and its lack of post - transcriptional correction mechanisms result in the rapid emergence of viral variants, difficulty in determining polymorphisms, and variants that contain substitutions associated with resistance and/or reduction of susceptibility towards new antivirals. The aim of this study was to map the polymorphisms in NS5A and NS5B and resistance mutations to new antiviral drugs in HCV strains with genotype 1a and 1b derived from patients with chronic hepatitis C infection. Serum samples from patients who underwent routine viral load tests and monitoring at the laboratory of viral hepatitis at the Adolfo Lutz Institute, São Paulo, Brazil were collected. A total of 698 and 853 samples were used for the characterization of NS5A and NS5B regions respectively; comprising HCV genotypes 1a and 1b. The prevalence of resistance mutations in the NS5A region was found to be 6.4%, with Y93H, L31M, Q30R, and Y93N as the main resistance-associated substitutions (RAS). No NS5B- associated RAS was observed for any of the drugs analyzed. This study reveals the presence of significant RAS in the HCV serum samples. These findings support the RAS test should be offered to individuals with poor response to double combination regimens prior to treatment initiation, thereby assisting strain vigilance and selection of effective treatment or retreatment options using DAA regimens.
Acupuncture for Prostatectomy Incontinence: Study Protocol for A Multicenter Single Blind Randomized Parallel Controlled Trial
Authors: Zhang Yao , Guo Shanqi , Wang Chaoran , Liu Xiaodi , Liu Yan , Shang Hongcai , Yang Peiying , Wang Liang , Zhai Jingbo , Li Xiaojiang , Jia Yingjie 
Published: June 2021

Abstract
Background: Urinary incontinence is a common complication after prostatectomy. Acupuncture is considered an effective treatment for prostatectomy incontinence (PPI), but evidence is still limited. We propose to evaluate the effectiveness of acupuncture in a rigorously conducted trial.Methods: Twenty hospitals will recruit 340 participants with urinary incontinence after prostatectomy in China from April 2021 to April 2022. Participants will be randomly allocated to acupuncture or sham acupuncture with a 1:1 ratio using computerized simple random sampling. The study plan consists of 1-week baseline, 6-week treatment, and 18-week follow up. Eighteen 30-mintute sessions of acupuncture or sham acupuncture treatment will be provided between weeks 1 and 6. The primary outcome is the change in the International Consultation on Incontinence Questionnaire-Urinary Incontinence Short Form (ICIQ-UI-SF) score at the week 6 from the baseline. Secondary outcomes include the change in volume of urine leakage at weeks 4 and 6 from a baseline measured using the 1-h Pad Test;72-h incontinence episode frequency based on a 72-h voiding diary; change in the Expanded prostate cancer Index Composite scale (EPIC-26); change in the Self-Rating Anxiety Scale; weekly consumption of pads; the severity of urinary incontinence based on a 72-h bladder diary and self-assessment of the therapeutic effect. The safety of acupuncture will also be assessed.Discussion: This trial will help to identify whether acupuncture is effective for PPI, and, if so, whether it exerts a therapeutic rather than a placebo effect.Trial Registration: The trial was registered on www.Chictr.org.cn. ChiCTR2100042500. Retrospectively registered on 22 January 2021.
Does a Multidisciplinary Menopausal Symptoms after Cancer Clinic Reduce Symptoms?
Authors: Hollingworth Jade , Walsh Lucy , Tran Stephanie , Ramage Lesley , Patel-Brown Shavita , Ambekar Manju , Weeks Jane , Williams Lucy , Cohen Paul A. 
Published: June 2021

Abstract
PurposeThis study aimed to measure the prevalence of menopausal symptoms in patients attending a multidisciplinary model of care clinic at their initial clinic visit and their subsequent follow-up consultation using a validated patient reported outcome measure to assess whether menopausal symptoms after cancer had improved.MethodsA retrospective review was conducted of patients attending the clinic in a 12-month period in 2017 (n=189). Recorded variables included patient demographics, details of index cancer, previous treatments and menopausal symptom management strategies. Severity of menopausal symptoms was evaluated using the Greene Climacteric Scale. The extent to which patients were bothered by symptoms were combined into two categories and dichotomized (present/absent). Differences in symptom prevalence between the initial consultation and first follow-up visit were examined using McNemar’s Test. ResultsThe majority of patients attending the clinic had a history of breast cancer (72%). 55% of patients were prescribed a non-hormonal therapy at their initial visit, most commonly gabapentin. Significantly fewer patients reported being bothered by hot flushes, fatigue, sleep difficulties and loss of interest in sex, anxiety or troubles concentrating at the first follow-up visit compared to their initial consultation (p < 0.01). ConclusionIn this study there was an improvement in self-reported menopausal symptoms in a significant proportion of cancer survivors attending a multidisciplinary menopause clinic between their initial and first subsequent follow-up consultations.
Transglutaminase 3 crosslinks secreted MUC2 and stabilizes the colonic mucus layer
Authors: Sharpen Jack , Dolan Brendan , Nyström Elisabeth , Birchenough George , Arike Liisa , Martinez-Abad Beatriz , Johansson Malin , Hansson Gunnar , Recktenwald Christian 
Published: June 2021

Abstract
The colonic mucus layer is organized as a two-layered system providing a physical barrier against pathogens and simultaneously harboring the commensal flora. The factors contributing to the organization of this gel network are not well understood. In this study, the impact of transglutaminase activity on this architecture was analyzed. Here, we show that transglutaminase TGM3 is the major TGM isoform expressed and synthesized in the colon. Furthermore, intrinsic extracellular TGM activity in the secreted mucus was demonstrated in vitro and ex vivo. Absence of this acyl-transferase activity resulted in faster degradation of the major mucus component the MUC2 mucin and changed the biochemical properties of mucus. Finally, TGM3-deficient mice showed an early increased susceptibility to DSS-induced colitis. Thus, these observations suggest that natural isopeptide cross-linking by TGM3 is important for mucus homeostasis and protection of the colon from inflammation, a suggested pre-stage of colon carcinoma.
Feasibility of a Fast-track Randomized Controlled Trial of Cell-free and Concentrated Ascites Reinfusion Therapy for Patients with Refractory Malignant Ascites
Authors: Yokomichi Naosuke , Imai Kengo , Sakamoto Masaki , Horiki Masashi , Yamauchi Toshihiro , Miwa Satoru , Inoue Satoshi , Uneno Yu , Suzuki Hidekazu , Wada Toru , Ichikawa Yuri , Morita Tatsuya 
Published: June 2021

Abstract
Purpose: Malignant ascites often causes discomfort in advanced cancer patients. Cell-free and concentrated ascites reinfusion therapy (CART) is one treatment modality, but controlled trials are lacking. We assessed the feasibility of a randomized controlled trial of CART vs. paracentesis alone for patients with refractory malignant ascites.Methods: This study was an open-label, fast-track, randomized controlled, feasibility trial. Patients admitted to four designated cancer hospitals who received no further anticancer treatments were eligible. Patients were randomly assigned 1:1 to a CART arm or control (simple paracentesis) arm. The feasibility endpoint was the percentage of patients who completed the study intervention. Secondary endpoints included paracentesis-free survival, patient request on the questionnaire for paracentesis (PRO-paracentesis)-free survival (the period until the patients first reported that they would want a paracentesis if indicated), and adverse events.Results: We screened 953 patients for eligibility. Of 61 patients with refractory malignant ascites, 21 patients were determined as eligible. Finally, 20 patients consented and were allocated; 18 patients (90%, 95% CI: 68.3-98.8) completed the study intervention. Median paracentesis-free survivals were 5 days (95% CI: 2-6) in the CART arm, and 6 days (3-9) in the control arm. Median PRO-paracentesis-free survivals were 4 days (2-5) and 5 days (1-9), respectively. One patient in the CART arm developed Grade 1 fever. Conclusion: A fast-track randomized controlled trial of CART for patients with malignant ascites is feasible. The efficacy and safety of CART should be assessed in future trials. PRO-paracentesis-free survival may be an outcome measure that complements paracentesis-free survival.
The mechanism of artemisinin resistance of Plasmodium falciparum malaria parasites originates in their initial transcriptional response.
Authors: Zhu Lei , Pluijm Rob W. van der , Kucharski Michal , Nayak Sourav , Tripathi Jaishree , Nosten François , Faiz Abul , Amaratunga Chanak , Lek Dysoley , Ashley Elizabeth A , Smithuis Frank , Phyo Aung Pyae , Lin Khin , Imwong Mallika , Mayxay Mayfong , Dhorda Mehul , Chau Nguyen Hoang , Thuy Nhien Nguyen Thanh Thuy , Newton Paul N , Jittamala Podjanee , Tripura Rupam , Pukrittayakamee Sasithon , Peto Thomas J , Miotto Olivo , von Seidlein Lorenz , Hien Tran Tinh , Ginsburg Hagai , Day Nicholas PJ , White Nicholas J. , Dondorp Arjen M , Bozdech Zbynek 
Published: June 2021

Abstract
The emergence and spread of artemisinin resistant Plasmodium falciparum, first in the Greater Mekong Subregion (GMS), and now in East Africa, is a major threat to global malaria eliminations ambitions. To investigate the artemisinin resistance mechanism, transcriptome analysis was conducted of 577 P. falciparum isolates collected in the GMS between 2016–2018. A specific artemisinin resistance-associated transcriptional profile was identified that involves a broad but discrete set of biological functions related to proteotoxic stress, host cytoplasm remodeling and REDOX metabolism. The artemisinin resistance-associated transcriptional profile evolved from initial transcriptional responses of susceptible parasites to artemisinin. The genetic basis for this adapted response is likely to be complex.
Cluster Synchronization in a Network of Nonlinear Systems with Directed Topology and Competitive Relationships
Authors: Wang Xin , Zhai Shidong , Luo Guoqiang , Huang Tao 
Published: June 2021

Abstract
This paper studies the cluster synchronization problem of coupled nonlinear systems with directed topology and competitive relationships. We assume that nodes within the same cluster have the same intrinsic dynamics, whereas node dynamics between different clusters differ. In the same cluster, there only exist cooperative relationships, and there may have competitive relationships among nodes belonging to different clusters. Under the assumptions that each node satisfies one-sided Lipschitz condition, and the digraphs of each cluster are strongly connected, some sufficient conditions for cluster synchronization in the cases of linear coupling and nonlinear coupling are obtained respectively. The obtained conditions are presented as some algebraic conditions which are easy to solve. Finally, our results are validated by two numerical simulations.
Bone Damage After Chemotherapy for Lymphoma: A Real-World Experience
Authors: S Mancuso , D Scaturro , M Santoro , G Di Gaetano , F Vitagliani , S Siragusa , S Gonnelli , G Letizia Mauro 
Published: June 2021

Abstract
Background: Despite recent improvements in survival due to advances in treatment, the quality of life of patients with lymphoma may be compromised by the long-term complications of chemotherapy and steroid therapy. Among these, a potentially relevant problem is bone loss and the development of fragility fractures.Aim: To provide further evidence of clinical or subclinical skeletal complications in correlation with biological variables and markers of bone disease in patients with complete response to therapy.Method: A cross-sectional observational study was conducted on subjects diagnosed with lymphoma with subsequent antineoplastic treatment, disease status after therapy defined as complete response disease for at least a year now. We performed: blood chemistry tests, imaging techniques (DEXA) and screening tools for the assessment of functional status and quality of life (SARC-F and mini-OQLQ).Results: Approximately 50% of the patients had osteoporosis. We found hypovitaminosis D and high PTH levels in most of the patients. We also found a high prevalence of vertebral fractures in 65.5% of cases. In the majority of patients, we found hypovitaminosis D and high levels of PTH. Furthermore, a statistically significant association between high PTH levels and previous lymphoma treatment. Finally, the Mini Osteoporosis Quality of Life questionnaire demonstrated a loss of quality of life as a consequence of the change in bone status.Conclusions: Patient treatment design for personalized chemotherapy would be desirable to reduce late effects on bone. Also, early prevention programs need to be applied before starting treatment. The most benefited subpopulations could be not only elderly but also young patients.
Compressing atmospheric data into its real information content
Authors: Kloewer Milan , Razinger Miha , Dominguez Juan , Dueben Peter , Palmer Tim 
Published: June 2021

Abstract
Hundreds of petabytes of data are produced annually at weather and climate forecast centres worldwide. Compression is inevitable to reduce storage and to facilitate data sharing. Current techniques do not distinguish the real from the false information in data. We define the bitwise real information content from information theory for data from the Copernicus Atmospheric Monitoring Service (CAMS). Most variables contain less than 7 bits of real information per value, which are also highly compressible due to spatio-temporal correlation. Rounding bits without real information to zero facilitates lossless compression algorithms and encodes the uncertainty within the data itself. The entire CAMS data is compressed by a factor of 17x, relative to 64-bit floats, while preserving 99% of real information. Combined with 4-dimensional compression to exploit the spatio-temporal correlation, factors beyond 60x are achieved without an increase in forecast errors. A data compression Turing test is proposed to optimize compressibility while minimizing information loss for the end use of weather and climate forecast data.
Trophic level decoupling drives future change in phytoplankton bloom phenology
Authors: Yamaguchi Ryohei , Rodgers Keith , Stein Karl , Timmermann Axel , Schlunegger Sarah , Bianchi Daniele , Dunne John , Slater Richard 
Published: June 2021

Abstract
Anthropogenic climate change is affecting marine ecosystems by altering the strength of phytoplankton blooms and driving shifts in the seasonality (phenology) of productivity. Here, we analyze a new 30-member Large Ensemble of climate change projections to quantify the sensitivity of phytoplankton bloom phenology (initiation, peak timing, and net growth period length) to anthropogenic forcing. Forced changes in the duration of net growth vary widely across the global ocean, with high latitudes experiencing a reduction of up to one month, and the tropics and subtropics experiencing an extension of up to one month. Changes in duration reflect shifts in both bloom initiation and peak bloom timing, which result from subtle decoupling between phytoplankton growth and zooplankton predation driven by temperature, nutrients and light variations. Changes in bloom strength and timing will alter the flow of energy in the marine ecosystem, with implications for higher trophic levels and fisheries.