bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptomic and proteomic analysis reveals mechanisms of low pollen-pistil compatibility during water lily cross breeding
Authors: Sun Chun-Qing , Chen Fa-Di , Teng Nian-Jun , Yao Yue-Mei , Shan Xi , dai zhongliang 
Published: December 2019

Abstract
Background: In water lily (Nymphaea) hybrid breeding, breeders often encounter non-viable seeds, which make it difficult to transfer desired or targeted genes of different Nymphaea germplasm. We found that pre-fertilization barriers were the main factor in the failure of the hybridization of Nymphaea. The mechanism of low compatibility between the pollen and stigma remains unclear; therefore, we studied the differences of stigma transcripts and proteomes at 0, 2, and 6 hours after pollination (HAP). Moreover, some regulatory genes and functional proteins that may cause low pollen-pistil compatibility in Nymphaea were identified. Results: RNA-seq was performed for three comparisons (2 vs 0 HAP, 6 vs 2 HAP, 6 vs 0 HAP), and the number of differentially expressed genes (DEGs) was 8,789 (4,680 were up-regulated), 6,401 (3,020 were up-regulated), and 11,284 (6,148 were up-regulated), respectively. Using label-free analysis, 75 (2 vs 0 HAP) proteins (43 increased and 32 decreased), nine (6 vs 2 HAP) proteins (three increased and six decreased), and 90 (6 vs 0 HAP) proteins (52 increased and 38 decreased) were defined as differentially expressed proteins (DEPs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the DEGs and DEPs were mainly involved in cell wall organization or biogenesis, S-adenosylmethionine (SAM) metabolism , hydrogen peroxide decomposition and metabolism, reactive oxygen species (ROS) metabolism, secondary metabolism, secondary metabolite biosynthesis, and phenylpropanoid biosynthesis. Conclusions: Our transcriptomic and proteomic analysis highlighted specific genes, incuding those in ROS metabolism, biosynthesis of flavonoids, SAM metabolism, cell wall organization or biogenesis and phenylpropanoid biosynthesis that warrant further study in investigations of the pollen-stigma interaction of water lily. This study strengthens our understanding of the mechanism of low pollen-pistil compatibility in Nymphaea at the molecular level, and provides a theoretical basis for overcoming the pre-fertilization barriers in Nymphaea in the future.
Development of a computer-based quantification method for immunohistochemically-stained tissues and its application to study mast cells in equine wound healing (proof of concept)
Authors: Dubuc Valerie , Laverty Sheila , Richard Hélène , Doré Monique , Theoret Christine 
Published: December 2019

Abstract
Background: There is a growing interest in the scientific community to use computer-based software programs for the quantification of cells during physiological and pathophysiological processes. Drawbacks of current computer-based methods used to quantify immunohistochemical staining are the complexity of use, expense of software and overly-simplified description of protocol thereby limiting reproducibility. The precise role of mast cells in equine cutaneous wound healing is unknown. Given the contribution of mast cells to the chronic inflammation observed in human keloid, a pathology similar to exuberant granulation tissue (EGT) in horses, mast cells might be present in high numbers in equine limb wounds predisposed to EGT. The main goal of this study was to develop a reliable and reproducible quantification method for immunostained tissues using a computer software that is widely available, at no cost, to the scientific community. At secondary goal was to conduct a proof of concept using the newly-established method to quantify mast cells during wound healing at different anatomical sites (body and limb) in horses to see if a different pattern is observed in limb wounds.Results: A good intraclass correlation coefficient (ICC, 0.67 p < 0.05) was found between the computer-based ImageJ method and manual counting. An excellent intra-operator ICC of 0.90 (p < 0.01) was found for the ImageJ quantification method while a good interoperator ICC of 0.69 (p < 0.01) was measured. Mast cells were localized below the epidermis, around cutaneous appendages and blood vessels. Mast cell numbers did not differ significantly in relation to anatomical location or time of healing.Conclusions: The computer-based quantification method developed is reliable, reproducible, available, cost-free and could be used to study different physiological and pathological processes using immunohistochemistry.
Social acceptance of alcohol use in Uganda.
Authors: Ssebunnya Joshua , Kituyi Caroline , Nabanoba Justine , Nakku Juliet , Bhana Arvin , Kigozi Fred 
Published: December 2019

Abstract

Background: Alcohol use is part of many cultural, religious and social practices, and provides perceived pleasure to many users. In many societies, alcoholic beverages are a routine part of the social landscape for many in the population. Relatively low rates were reported for Alcohol Use Disorders (AUD) in a community based survey and facility detection survey conducted in the study site contrary to findings in earlier formative studies where alcohol use was reported to be a major health problem. The aim of this study was to understand reasons for under-reporting and the low detection rate for AUDs, exploring the societal perceptions of alcohol use in the study district. Methods: The study was conducted in Kamuli District (implementation site for the PRIME project). Semi-structured interviews and focus group discussions were conducted with purposively selected participants that included local and religious leaders, lay people, health workers as well as heavy alcohol drinkers and their spouses. Interviews were tape-recorded and transcribed verbatim. The analysis followed 4 thematic areas, which include the extent and acceptability of alcohol use, patterns of alcohol use, perceived health problems associated with alcohol use and help-seeking behavior for persons with alcohol related problems. Results: The findings indicate that alcohol consumption in the study site was common and widely acceptable across all categories of people, with minimal restrictions. Society tends to overlook problems associated with alcohol use except when it is life-threatening. Help-seeking for such problems was therefore reported to be relatively rare. Conclusion: Alcohol was readily available in the community and its consumption widely acceptable with minimal restrictions to the minors. There is low recognition of alcohol use related health problems, resulting in poor help-seeking behavior. Key words: Alcohol, Kamuli, Alcohol Use Disorder, PRIME acceptability
First referral to an Integrated Onco-Palliative Care program: a retrospective analysis of its timing
Authors: Barth Claire , Colombet Isabelle , Montheil Vincent , Huillard Olivier , Boudou-Rouquette Pascaline , Tlemsani Camille , Alexandre Jérôme , Goldwasser François , Vinant Pascale 
Published: December 2019

Abstract
Background: Palliative care (PC) referral is recommended early in the course of advanced cancer. This study aims to describe, in an integrated onco-palliative care program (IOPC), patient’s profile when first referred to this program, timing of this referral and its impact on the trajectory of care at end-of-life.Patients and Methods: The IOPC combined the weekly onco-palliative meeting (OPM) dedicated to patients with incurable cancer, and/or the clinical evaluation by the PC team. Oncologists can refer to the multidisciplinary board of the OPM the patients for whom goals and organization of care need to be discussed. We analyzed all patients first referred at OPM in 2011-2013. We defined the index of precocity (IP), as the ratio of the time from first referral to death by the time from diagnosis of incurability to death, ranging from 0 (late referral) to 1 (early referral).Results: Of the 416 patients included, 57% presented with lung, urothelial cancers, or sarcoma. At first referral to IOPC, 76% were receiving antitumoral treatment, 63% were outpatients, 56% had a performance status ≤2 and 46% had a serum albumin level >35g/l. The median [1st-3rd quartile] IP was 0.39 [0.16-0.72], ranging between 0.53 [0.20-0.79] (earliest, for lung cancer) to 0.16 [0.07-0.56] (latest relatively to length of metastatic disease, for prostate cancer). Among 367 decedents, 42 (13%) received antitumoral treatment within 14 days before death, and 157 (43%) died in PC units.Conclusions: The IOPC is an effective organization to enable early integration of PC and decrease aggressiveness of care near the end-of life. The IP is a useful tool to model the timing of referral to IOPC, while taking into account each cancer types and therapeutic advances.
Post-Traumatic Stress Disorder in Italy: a comprehensive evaluation of all the ICD comorbidities and gender-related differences
Authors: Ferretti Fabio , Pozza Andrea , Bossini Letizia , Desantis Serena , Olivola Miriam , Matto Laura Del , Gualtieri Giacomo , Gusinu Roberto , Bezzini Daiana , Fagiolini Andrea , Coluccia Anna 
Published: December 2019

Abstract
Objectives: The association between Post-Traumatic Stress Disorder (PTSD) and physical comorbidities is controversial since most studies focused on specific comorbidity and victim types. In Italy, data on this issue are scarce. A comprehensive evaluation of all the ICD categories co-occurring in PTSD may orient assessment and treatment during clinical and forensic practice. This is the first study evaluating all the ICD physical comorbidities and gender-related differences in Italian PTSD patients. Eighty-four PTSD patients (36 females, 48 males) were included. The Clinician-Administered PTSD Scale, Mini International Neuropsychiatric Interview and Davidson Trauma Scale were administered. Results: Most patients had a PTSD consequent to an accident and half of them presented extreme severity. No gender differences emerged on symptom severity/duration and age at the event. Metabolic (39.29%), circulatory (20.24%) and musculoskeletal diseases (17.86%) were the most frequent comorbidities. Metabolic/circulatory diseases were more frequent among males ( p =0.019 and p = 0.027, respectively) while females more frequently showed neoplasms ( p =0.039). Physical comorbidities represent a serious complication in PTSD patients and are more prevalent than in general population. While gender is not associated with symptom presentation, it seems to play a key role in specific comorbidities including metabolic, circulatory and neoplastic diseases.
Comparative transcriptome analysis reveals the molecular regulation underlying the adaptive mechanism of cherry (Cerasus pseudocerasus Lindl.) to shelter covering
Authors: Tian Tian , Qiao Guang , Wen Zhuang , Deng Bin , Qiu Zhilang , Hong Yi , Wen Xiaopeng 
Published: December 2019

Abstract
Background: Rain-shelter covering is widely applied during cherry fruit development in subtropical monsoon climates with the aim of decreasing the dropping and cracking of fruit caused by excessive rainfall. Under rain-shelter covering, the characteristics of the leaves and fruit of the cherry plant may adapt to the changes in the microclimate. However, the molecular mechanism underlying such adaptation remains unclear, although clarifying it may be helpful for improving the yield and quality of cherry under rain-shelter covering.
Results: To better understand the regulation and adaptive mechanism of cherry under rain-shelter covering, 38,621 and 3,584 differentially expressed genes were identified with a combination of Illumina HiSeq and single-molecule real-time sequencing in leaves and fruits, respectively, at three developmental stages. Among these, key genes, such as those encoding photosynthetic-antenna proteins (Lhca and Lhcb) and photosynthetic electron transporters (PsbP, PsbR, PsbY, and PetF), were up-regulated following the application of rain-shelter covering, leading to increased efficiency of light utilization. The mRNA levels of genes involved in carbon fixation, namely, rbcL and rbcS, were clearly increased compared with those under shelter-free conditions, resulting in improved CO2 utilization. Furthermore, the transcription levels of genes involved in chlorophyll (hemA, hemN, and chlH) and carotenoid synthesis (crtB, PDS, crtISO, and lcyB) in the sheltered leaves peaked earlier than those in the unsheltered leaves, thereby promoting organic matter accumulation in leaves. Remarkably, the expression levels of key genes involved in the metabolic pathways of phenylpropanoid (PAL, C4H, and 4CL) and flavonoid (CHS, CHI, F3’H, DFR, and ANS) in the sheltered fruits were also up-regulated earlier than of those in the unsheltered fruits, conducive to an increase in anthocyanin content in the fruits.
Conclusions: According to the physiological indicators and transcriptional expression levels of the related genes, the adaptive regulation mechanism of cherry plants was systematically revealed. These findings can help understand the effect of rain-shelter covering on Chinese cherry cultivation in rainy regions.
Effects of non-surgical periodontal therapy on systemic inflammation and metabolic markers in patients undergoing haemodialysis and/or peritoneal dialysis: a systematic review and meta-analysis
Authors: Author) Hui Yue(Former Corresponding , Xu Xinxin , Liu Qin , Li Xiaozhi , Xiao Yiting , Author) Bo Hu(New Corresponding 
Published: December 2019

Abstract
Background: This systematic review aimed to investigate whether non-surgical periodontal therapy (NSPT) can reduce systemic inflammatory levels and improve metabolism in patients undergoing haemodialysis (HD) and/or peritoneal dialysis (PD). Methods: Electronic databases (PubMed, EMBASE, CENTRAL, NCKI, and WFPD) were searched for randomized controlled trials (RCTs) performed through July 2019. The risk of bias within studies was assessed with the Cochrane Collaboration’s risk assessment tool. The systemic inflammatory and metabolic outcomes included the highly sensitive C-reactive protein (hs-CRP), interleukin 6 (IL-6), tumour necrosis factor-α (TNF-a), the albumin (Alb), and lipid metabolite levels. Meta-analyses (MAs) were performed to calculate the overall effect size where appropriate. Results: Five RCTs were included in this study. Compared with untreated periodontitis groups, the dialysis patients after NSPT significantly showed decreased hs-CRP levels at less than or equal to 2- (standardized mean difference (SMD) -1.53, 95% confidence interval (CI) -2.95 to -0.11), 3- (-0.27, 95% CI -0.47 to -0.07), and 6 months (-0.36, 95% CI -0.55 to -0.17), respectively. No significant difference was found in IL-6 and Alb levels following NSPT at either the 3- or 6- month of follow-ups. No MAs could be performed on TNF-a level and the lipid metabolic markers. No adverse effects were observed in any of the studies. Conclusions: NSPT can moderately reduce serum hs-CRP levels in HD and/or PD patients, but did not significantly change IL-6 or Alb levels. For TNF-a and lipid metabolism markers, no sufficient evidence supports that these levels are changed after NSPT. Additional scientific research is necessary to assess the effects of NSPT on systemic inflammation and metabolic parameters in dialysis patients.
Molecular characterization and expression analysis of pitaya (Hylocereus polyrhizus) HpLRR genes in response to Neoscytalidium dimidiatuminfection
Authors: Xu Min , Liu Cheng-Li , Fu Yu , Liao Zhi-Wen , Guo Pan-Yang , Xiong Rui , Cheng Yu , Wei Shuang-Shuang , Huang Jia-Quan , Tang Hua 
Published: December 2019

Abstract
Background:Canker disease caused by Neoscytalidium dimidiatumis a devastating disease resulting in a major loss to the pitaya industry. However, resistance proteins in plants play crucial roles to against pathogen infection. Among resistance proteins, the leucine-rich repeat (LRR) protein is a major family that plays crucial roles in plant growth, development, and biotic and abiotic stress responses, especially in disease defense.
Results: In the present study, a transcriptomics analysis identified a total of 272 LRR genes, 233 of which had coding sequences (CDSs), in the plant pitaya (Hylocereus polyrhizus) in response to fungal Neoscytalidium dimidiatuminfection. These genes were divided into various subgroups based on specific domains and phylogenetic analysis. Molecular characterization, functional annotation of proteins, and an expression analysis of the LRR genes were conducted. Additionally, four LRR genes (CL445.Contig4_All, Unigene28_All, CL28.Contig2_All, and Unigene2712_All, which were selected because they had the four longest CDSs were further assessed using quantitative reverse transcription PCR (qRT-PCR) at different fungal infection stages in different pitaya species (Hylocereus polyrhizus and Hylocereus undatus), in different pitaya tissues, and after treatment with salicylic acid (SA), methyl jasmonate (MeJA), and abscisic acid(ABA) hormones. The associated protein functions and roles in signaling pathways were identified.
Conclusions: This study provides a comprehensive overview of the HpLRR family genes at transcriptional level in pitaya in response toN. dimidiatuminfection, it will be helpful to understand the molecular mechanism of pitaya canker disease, and lay a strong foundation for further research.
Low red/far-red ratio as a signal promotes carbon assimilation of soybean seedlings by increasing the photosynthetic capacity
Authors: Yang Feng , Liu Qinlin , Cheng Yajiao , Feng Lingyang , Wu Xiaoling , Fan Yuanfang , Raza Muhammad Ali , Wang Xiaochun , Yong Taiwen , Liu Weiguo , Liu Jiang , Du Junbo , Shu Kai , Yang Wenyu 
Published: December 2019

Abstract
Background: Shading includes low light intensity and varying quality. However, a low red/far-red (R/Fr) ratio of light is a signal that affects plant growth in intercropping and close- planting systems. Thus, the low R/Fr ratio uncoupling from shading conditions was assessed to identify the effect of light quality on photosynthesis and CO2 assimilation. Soybean plants were grown in a growth chamber with natural solar radiation under four treatments, that is, normal (N, sunlight), N+Fr, Low (L) +Fr, and L light.

Results: Low R/Fr ratio significantly increased the total biomass, leaf area, starch and sucrose contents, chlorophyll content, net photosynthetic rate, and quantum efficiency of the photosystem II compared with normal R/Fr ratio under the same light level (P < 0.05). Proteomic analysis of soybean leaves under different treatments was performed to quantify the changes in photosynthesis and CO2 assimilation in the chloroplast. Among the 7834 proteins quantified, 12 showed a > 1.3-fold change in abundance, of which 1 was related to porphyrin and chlorophyll metabolism, 2 were involved in photosystem I (PS I), 4 were associated with PS II, 3 proteins participated in photosynthetic electron transport, and 2 were involved in starch and sucrose metabolism. The dynamic change in these proteins indicates that photosynthesis and CO2 assimilation were maintained in the L treatment by up-regulating the component protein levels compared with those in N treatment. Although low R/Fr ratio increased the photosynthetic CO2 assimilation parameters, the differences in most protein expression levels in N+Fr and L+Fr treatments compared with those in N treatment were insignificant. Similar trends were found in gene expression through quantitative reverse transcription polymerase chain reaction excluding the gene expression of sucrose synthase possible because light environment is one of the factors affecting carbon assimilation.
Conclusions: Low R/Fr ratio (high Fr light) can increase the photosynthetic CO2 assimilation in the same light intensity by improving the photosynthetic efficiency of the photosystems.
A prospective study of erectile dysfunction in men after pelvic surgical procedures and its association with non - modifiable risk factors
Authors: Artemi Sofia , Vassiliu Panteleimon , Arkadopoulos Nikolaos , Smyrnioti Maria - Eleni , Sarafis Pavlos , Smyrniotis Vasileios 
Published: December 2019

Abstract
Objective: A pelvic surgery can cause erectile dysfunction. The purpose of this study was to evaluate erectile function at various times after pelvic surgery in male patients; to search the non-modifiable risk factors associated with the presence and intensity of sexuality in these patients. This prospective study used the erectile dysfunction IIEF scale.
Results: The study population comprised of 106 male patients who had undergone minor pelvic surgery at least 9 months before and during the 2010–2016 period in the 4th Surgical Clinic. A control group of healthy males (N=106) who underwent no pelvic surgery matched for age was also used for reference values. The main age of the participants was 66.16 ±13.07 years old. A history of colectomy was present in 36.8%, 18.9% had undergone sigmoidectomy, and 33% inguinal hernia repair. The percentage of severe erectile function increased from 38.7% before surgery to 48.1% (25% increase) after surgery, at the end of the follow-up period (p<0.05). In the multivariate analysis model, age emerged as an independent predictor of erectile function (p<0.001). Age was the most important determinant of the IIEF score, which was aggravated by 25% from the first to the last assessment of patients.
The added value of parenchymal transcranial Doppler sonography at the Emergency Room: case report of an unusual gait disorder
Authors: Godani Massimiliano , Lanza Giuseppe , Bella Rita , Trevisan Lucia , Ferri Raffaele 
Published: December 2019

Abstract
Background: the growing application of parenchymal transcranial Doppler sonography (pTCS) helps the diagnosis of a wide range of neurological diseases, especially movement disorders. Here, we report a patient with an unusual gait disorder in whom pTCS performed at the Emergency Room rapidly provided diagnostic clues towards a degenerative movement disorder. Case presentation: A 60-year old man presented at the Emergency Room with a rapidly progressive history of walking difficulty, without falls. He had no family history of neurodegenerative or psychiatric diseases. Because of a depressive disorder arisen one year earlier, he was under oral treatment with escitalopram 10 mg and amisulpride 100 mg daily. Neurological examination showed a gait characterized by ataxia, rigidity, and limping; he also had mild oro-facial and hands dyskinesia, some of which were also present during walking. Brain computed tomography was normal. A pTCS performed at the Emergency Room showed hyperechogenicity of the substantia nigra and the caudate nucleus, bilaterally. This pattern is suggestive of Huntington’s disease (HD), as confirmed by the molecular genetic test carried out later. Other laboratory tests, standard electroencephalogram, and 1.5-T brain MRI were normal.Conclusions: to date, this is the first report of HD sonographically detected at the Emergency Room. This supports the view that pTCS can be easily implemented in the diagnostic algorithm and differential diagnosis of movement disorders even in an urgency setting. Notably, conventional MRI did not detect, at this stage, any abnormality; this further highlights the diagnostic utility of pTCS, which also allowed to exclude a drug-induced effect or a different movement disorder. In clinically suspected cases, pTCS can extend the neurological examination by providing diagnostic clues more rapidly and less expensively than neuroimaging.