bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frequent contiguous pattern mining over biological sequences of protein misfolded diseases
Authors: Islam Mohammad Shahedul , Mia Md. Abul Kashem , Rahman Mohammad Shamsur , Arefin Mohammad Shamsul , Dhar Pranab Kumar , Koshiba Takeshi 
Published: September 2021

AbstractBackgroundProteins are integral part of all living beings, which are building blocks of many amino acids. To be functionally active, amino acids chain folds up in a complex way to give each protein a unique 3D shape, where a minor error may cause misfolded structure. Genetic disorder diseases i.e.Alzheimer, Parkinson,etc. arise due to misfolding in protein sequences. Thus, identifying patterns of amino acids is important for inferring protein associated genetic diseases. Recent studies in predicting amino acids patterns focused on only simple protein misfolded disease i.e.Chromaffin Tumor, by association rule mining. However, more complex diseases are yet to be attempted. Moreover, association rules obtained by these studies were not verified by usefulness measuring tools.ResultsIn this work, we analyzed protein sequences associated with complex protein misfolded diseases (i.e.Sickle Cell Anemia, Breast Cancer, Cystic Fibrosis, Nephrogenic Diabetes Insipidus,andRetinitis Pigmentosa 4) by association rule mining technique and objective interestingness measuring tools. Experimental results show the effectiveness of our method.ConclusionAdopting quantitative experimental methods, this work can form more reliable, useful and strong association rules i. e. dominating patterns of amino acid of complex protein misfolded diseases. Thus, in addition to usual applications, the identified patterns can be more useful in discovering medicines for protein misfolded diseases and thereby may open up new opportunities in medical science to handle genetic disorder diseases.
Genome-wide association study reveals the genetic architecture of root hair length in maize
Authors: Liu Lin , Jiang Lu-Guang , Luo Jin-Hong , Xia Ai-Ai , Chen Li-Qun , He Yan 
Published: September 2021

Abstract
Background
Root hair, a special type of tubular-shaped cell, outgrows from root epidermal cell and plays important roles in the acquisition of nutrients and water, as well as interactions with biotic and abiotic stress. Although many genes involved in root hair development have been identified, genetic basis of natural variation in root hair growth has never been explored.

Results
Here, we utilized a maize association panel including 281 inbred lines with tropical, subtropical, and temperate origins to decipher the phenotypic diversity and genetic basis of root hair length. We demonstrated significant associations of root hair length with many metabolic pathways and other agronomic traits. Combining root hair phenotypes with 1.25 million single nucleotide polymorphisms (SNPs) via genome-wide association study (GWAS) revealed several candidate genes implicated in cellular signaling, polar growth, disease resistance and various metabolic pathways.

Conclusions
These results illustrate the genetic basis of root hair length in maize, offering a list of candidate genes predictably contributing to root hair growth, which are invaluable resource for the future functional investigation.
Integrated analysis of lncRNA and mRNA in liver of Megalobrama amblycephala post Aeromonas hydrophila infection
Authors: Sun Qianhui , Wang Jixiu , Wang Guowen , Wang Huanling , Liu Hong 
Published: September 2021

Abstract
Background
As non-coding RNA molecules of more than 200 bp in length, long non-coding RNAs (lncRNAs) play a variety of roles in biological processes, including regulating the immune responses to bacterial infections. In recent years, there have been many in-depth studies on mammalian lncRNAs, but the relevant studies in fish are very limited. Meanwhile, since lncRNAs are not conserved among species, it is difficult to apply the existing results directly to unstudied species.

Results
To obtain the information of lncRNAs in Megalobrama amblycephala, one of the most economically important freshwater fish in China, also to better understand the biological significance of lncRNAs in the immunity system, the fish liver at 0, 4, 12, 24, and 72 h post Aeromonas hydrophila infection (hpi) were obtained for lncRNA-sequencing (lncRNA-seq). A total of 14,849 lncRNAs were identified, and 2196 lncRNAs showed significant differences at different time points post A. hydrophila infection. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the target genes of the differentially expressed lncRNAs were enriched in several pathways related to immune such as apoptosis, inflammation, and immune response. Time-specific modules were then identified, using weighted correlation network analysis (WGCNA), and 28 modules significantly correlated with different time point after infection were found. Furthermore, four immune-related genes and six lncRNAs in the time-specific modules were subsequently verified by RT-qPCR.

Conclusions
The above findings reveal the discovery of widespread differentially expressed lncRNAs in the M. amblycephala liver post A. hydrophila infection, suggesting that lncRNAs might participate in the regulation of host response to bacterial infection, enriching the information of lncRNAs in teleost and providing a resources basis for further studies on the immune function of lncRNAs.
Morphological characteristics and transcriptome analysis at different anther development stages of the male sterile mutant MS7–2 in Wucai (Brassica campestris L.)
Authors: Wang Jian , Yang Yitao , Zhang Lei , Wang Shaoxing , Yuan Lingyun , Chen Guohu , Tang Xiaoyan , Hou Jinfeng , Zhu Shidong , Wang Chenggang 
Published: September 2021

Abstract
Background
The discovery of male sterile materials is of great significance for the development of plant fertility research. Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a variety of non-heading Chinese cabbage. There are few studies on the male sterility of wucai, and the mechanism of male sterility is not clear. In this study, the male sterile mutant MS7–2 and the wild-type fertile plant MF7–2 were studied.

Results
Phenotypic characteristics and cytological analysis showed that MS7–2 abortion occurred at the tetrad period. The content of related sugars in the flower buds of MS7–2 was significantly lower than that of MF7–2, and a large amount of reactive oxygen species (ROS) was accumulated. Through transcriptome sequencing of MS7–2 and MF7–2 flower buds at three different developmental stages (a–c), 2865, 3847, and 4981 differentially expressed genes were identified in MS7–2 at the flower bud development stage, stage c, and stage e, respectively, compared with MF7–2. Many of these genes were enriched in carbohydrate metabolism, phenylpropanoid metabolism, and oxidative phosphorylation, and most of them were down-regulated in MS7–2. The down-regulation of genes involved in carbohydrate and secondary metabolite synthesis as well as the accumulation of ROS in MS7–2 led to pollen abortion in MS7–2.

Conclusions
This study helps elucidate the mechanism of anther abortion in wucai, providing a basis for further research on the molecular regulatory mechanisms of male sterility and the screening and cloning of key genes in wucai.
Risk factors and in-hospital mortality of postoperative hyperlactatemia in patients after acute type A aortic dissection surgery
Authors: Wang Su , Wang Dashuai , Huang Xiaofan , Wang Hongfei , Le Sheng , Zhang Jinnong , Du Xinling 
Published: September 2021

Abstract
Background
Hyperlactatemia may be caused by increased production due to tissue hypoxia or non-hypoxia. The aim of this study was first to identify risk factors for postoperative hyperlactatemia (POHL) after Stanford type A acute aortic dissection surgery (AADS) and construct a predictive model, and second to evaluate the impact of POHL on prognosis.

Methods
This retrospective study involved patients undergoing AADS from January 2016 to December 2019 in Wuhan Union Hospital. Multivariate logistic regression analysis was performed to identify independent risk factors for POHL. A nomogram predicting POHL was established based on these factors and was validated in the original dataset. The receiver operating characteristic curve was drawn to assess the ability of postoperative lactate levels to predict the in-hospital mortality.

Results
A total of 188 patients developed POHL after AADS (38.6%). Male gender, surgery history, red blood cell transfusion and cardiopulmonary bypass time were identified as independent predictors. The C-index of the prediction model for POHL was 0.72, indicating reasonable discrimination. The model was well calibrated by visual inspection and goodness-of-fit test (Hosmer–Lemeshow χ2 = 10.25, P = 0.25). Decision and clinical impact curves of the model showed good clinical utility. The overall in-hospital mortality rate was 10.1%. Postoperative lactate levels showed a moderate predictive power for postoperative in-hospital mortality (C-index: 0.72).

Conclusion
We developed and validated a prediction model for POHL in patients undergoing AADS, which may have clinical utility in personal risk evaluation and preventive interventions. The POHL could be a good predictor for in-hospital mortality.
Strategies to maximise study retention and limit attrition bias in a prospective cohort study of men reporting a history of injecting drug use released from prison: the prison and transition health study
Authors: Stewart Ashleigh Cara , Cossar Reece , Walker Shelley , Wilkinson Anna Lee , Quinn Brendan , Dietze Paul , Winter Rebecca , Kirwan Amy , Curtis Michael , Ogloff James R. P. , Kinner Stuart , Aitken Campbell , Butler Tony , Woods Emma , Stoové Mark 
Published: September 2021

Abstract
Background
There are significant challenges associated with studies of people released from custodial settings, including loss to follow-up in the community. Interpretation of findings with consideration of differences between those followed up and those not followed up is critical in the development of evidence-informed policies and practices. We describe attrition bias in the Prison and Transition Health (PATH) prospective cohort study, and strategies employed to minimise attrition.

Methods
PATH involves 400 men with a history of injecting drug use recruited from three prisons in Victoria, Australia. Four interviews were conducted: one pre-release (‘baseline’) and three interviews at approximately 3, 12, and 24 months post-release (‘follow-up’). We assessed differences in baseline characteristics between those retained and not retained in the study, reporting mean differences and 95% confidence intervals (95% CIs).

Results
Most participants (85%) completed at least one follow-up interview and 162 (42%) completed all three follow-up interviews. Retained participants were younger than those lost to follow-up (mean diff − 3.1 years, 95% CI -5.3, − 0.9). There were no other statistically significant differences observed in baseline characteristics.

Conclusion
The high proportion of participants retained in the PATH cohort study via comprehensive follow-up procedures, coupled with extensive record linkage to a range of administrative datasets, is a considerable strength of the study. Our findings highlight how strategic and comprehensive follow-up procedures, frequent contact with participants and secondary contacts, and established working relationships with the relevant government departments can improve study retention and potentially minimise attrition bias.
The general practitioners perspective regarding registration of persistent somatic symptoms in primary care: a survey
Authors: Kitselaar Willeke M. , van der Vaart Rosalie , van Tilborg-den Boeft Madelon , Vos Hedwig M. M. , Numans Mattijs E. , Evers Andrea W. M. 
Published: September 2021

Abstract
Background
Persistent somatic symptoms (PSS) are common in primary care and often accompanied by an increasing disease burden for both the patient and healthcare. In medical practice, PSS is historically considered a diagnosis by exclusion or primarily seen as psychological. Besides, registration of PSS in electronic health records (EHR) is ambiguous and possibly does not reflect classification adequately. The present study explores how general practitioners (GPs) currently register PSS, and their view regarding the need for improvements in classification, registration, and consultations.

Method
Dutch GPs were invited by email to participate in a national cross-sectional online survey. The survey addressed ICPC-codes used by GPs to register PSS, PSS-related terminology added to free text areas, usage of PSS-related syndrome codes, and GPs’ need for improvement of PSS classification, registration and care.

Results
GPs (n = 259) were most likely to use codes specific to the symptom presented (89.3%). PSS-related terminology in free-text areas was used sparsely. PSS-related syndrome codes were reportedly used by 91.5% of GPs, but this was primarily the case for the code for irritable bowel syndrome. The ambiguous registration of PSS is reported as problematic by 47.9% of GPs. Over 56.7% of GPs reported needing additional training, tools or other support for PSS classification and consultation. GPs also reported needing other referral options and better guidelines.

Conclusions
Registration of PSS in primary care is currently ambiguous. Approximately half of GPs felt a need for more options for registration of PSS and reported a need for further support. In order to improve classification, registration and care for patients with PSS, there is a need for a more appropriate coding scheme and additional training.
A rare case of coexistence of Wegener’s granulomatosis and pulmonary tuberculosis with subsequent development of thrombosis of the cerebral veins
Authors: Rostami Zohreh , Cegolon Luca , Jafari Nematollah Jonaidi , Gholami Nasrin , Mousavi Seyed Vahid , Allahyari Fakhri , Azami Atena , Javanbakht Mohammad 
Published: September 2021

Abstract
Background
Granulomatosis with polyangiitis (GPA), also known as Wegener’s granulomatosis, is an idiopathic systemic disease typically affecting the lungs, although other organs may also be involved.

Case presentation
A 28-year-old male was admitted to Baqiyatallah university hospital in Teheran (Iran) after a 3-week history of fever and productive cough. The patient gradually developed fatigue, arthralgia, hematuria, nausea, vomiting, dyspnea, hemoptysis, weight loss, oliguria and then anuria. Chest-X-ray (CXR) and computerized tomography scan revealed cavitating nodular opacities in the right lung lobe. Furthermore, plasma creatinine increased from 2.2 to 4 mg/dl in a few days. Histopathological examination of kidney biopsy revealed peri-glomerular and peri-vascular inflammation, degeneration and necrosis of the tubular epithelial lining, red blood cell casts, distorted glomerular structure, fibrin thrombi, segmental breaks of the glomerular basal membrane, disruption of Bowman's capsular membrane and crescent formation of the affected glomeruli. An abnormal CXR, an abnormal urinary sediment and a typical kidney histology were used as criteria to diagnose glomerulonefritis with poliangiitis (GPA). Bronchoalveolar lavage smear and PCR turned out positive for mycobacterium tuberculosis. After 3 months of treatment for (GPA) and tuberculosis the patient developed headache and seizure. Cerebral Magnetic Resonance Venography revealed cerebral venous thrombosis of the sinus transverse and sigmoid.

Conclusions
Tuberculosis may coexist with GPA, as it occurred in our patient. Since a crescentic glomerulonephritis can progress to renal failure, clinicians should always be aware of potential multiple conditions when considering differential diagnoses.
Prevalence and risk factors for exposure to Toxoplasma gondii in slaughterhouse workers in western Kenya
Authors: Cook Elizabeth Anne Jessie , Gitahi Nduhiu , de Glanville William Anson , Thomas Lian F. , Kariuki Samuel , Kang’ethe Erastus , Fèvre Eric Maurice 
Published: September 2021

AbstractBackgroundToxoplasma gondiiis a zoonotic protozoan parasite infecting warm-blooded animals. Infection in people can occur through ingestion of oocysts passed in the faeces of the definitive hosts; ingestion of bradyzoites in the tissue of infected intermediate hosts; or exposure to tachyzoites in raw milk and eggs. Slaughterhouse workers are considered a high-risk group forT. gondiiexposure because of their contact with raw meat, although a positive relationship between handling raw meat andT. gondiiseropositivity has not been demonstrated in all studies. This study aimed to determine the seroprevalence of antibodies toT. gondiiin slaughterhouse workers in Kenya and identify risk factors associated with seropositivity.MethodsA survey of slaughterhouse workers was conducted in 142 slaughter facilities in the study area. Information regarding demographics, contact with livestock, meat consumption, and practices in the slaughterhouse was collected using structured questionnaires. Commercial ELISAs were used to detect IgM and IgG antibodies againstT. gondiiand a multi-level logistic regression model was used to identify potential risk factors for seropositivity in slaughterhouse workers.ResultsThe apparent prevalence of antibodies toT. gondiiwas 84.0% (95% Confidence Interval (CI) 81.2–86.5%) for IgG and 2.2% (95% CI 1.3–3.5%) for IgM antibodies. All IgM positive individuals were IgG positive. Risk factors for exposure toT. gondiiwere: increasing age (Odds Ratio (OR) 1.03; 95% CI 1.01–1.05); owning poultry (OR 2.00; 95% CI 1.11–3.62); and consuming animal blood (OR 1.92; 95% CI 1.21–3.03).ConclusionsThe seroprevalence of antibodies toT. gondiiwas very high in this population and considerably higher than published values in the general population. Risk factors included age, owning poultry and drinking animal blood which were consistent with previous reports but none were specifically associated with working in the slaughterhouse. In this instance slaughterhouse workers may represent a useful sentinel for the general population where the level of exposure is also likely to be high and may signify an unidentified public health risk to vulnerable groups such as pregnant women. A detailed understanding of the epidemiology of infection is required, which should include an assessment of incidence, mortality, and burden sinceT. gondiiinfection is likely to have life-long sequelae.
Postoperative morbidity and quality of life between totally laparoscopic total gastrectomy and laparoscopy-assisted total gastrectomy: a propensity-score matched analysis
Authors: Park Shin-Hoo , Suh Yun-Suhk , Kim Tae-Han , Choi Yoon-Hee , Choi Jong-Ho , Kong Seong-Ho , Park Do Joong , Lee Hyuk-Joon , Yang Han-Kwang 
Published: September 2021

Abstract
Background
This study aimed to evaluate the surgical outcome and quality of life (QoL) of totally laparoscopic total gastrectomy (TLTG) compared with laparoscopy-assisted total gastrectomy (LATG) in patients with clinical stage I gastric cancer.

Methods
From 2012 to 2018, EGC patients who underwent TLTG (n = 223), including the first case with intracorporeal hemi-double stapling, were matched to those who underwent LATG (n = 114) with extracorporeal circular stapling, using 2:1 propensity score matching (PSM). Prospectively collected morbidity was compared between the TLTG and LATG groups in conjunction with the learning curve. The European Organization for Research and Treatment of Cancer (EORTC) QoL questionnaires QLQ-C30, STO22, and OG25 were prospectively surveyed during postoperative 1 year for patient subgroups.

Results
After PSM, grade I pulmonary complication rate was lower in the TLTG group (n = 213) than in the LATG group (n = 111) (0.5% vs. 5.4%, P = 0.007). Other complications were not different between the groups. The learning curve of TLTG was overcome at the 26th case in terms of the comprehensive complication index. The TLTG group after learning curve showed lower grade I pulmonary complication rate than the matched LATG group (0.5% vs. 4.7%, P = 0.024). Regarding postoperative QoL, the TLTG group (n = 63) revealed less dysphagia (P = 0.028), pain (P = 0.028), eating restriction (P = 0.006), eating (P = 0.004), odynophagia (P = 0.023) than the LATG group (n = 21). Multivariate analyses for each QoL item demonstrated that TLTG was the only common independent factor for better QoL.

Conclusions
TLTG reduced grade I pulmonary complications and provided better QoL in dysphagia, pain, eating, odynophagia than LATG for patients with clinical stage I gastric cancer.
Estrogen markedly reduces circulating low-density neutrophils and enhances pro-tumoral gene expression in neutrophil of tumour-bearing mice
Authors: Lim Chew Leng , Lin Valerie C.-L. 
Published: September 2021

Abstract
Background
Neutrophils are important for immune surveillance of tumour cells. Neutrophils may also be epigenetically programmed in the tumour microenvironment to promote tumour progression. In addition to the commonly known high-density neutrophils (HDN) based on their separation on density gradient, recent studies have reported the presence of high levels of low-density neutrophils (LDN) in tumour-bearing mice and cancer patients. We reported previously that estrogen promotes the growth of estrogen receptor α-negative mammary tumours in mice undergoing mammary involution through stimulating pro-tumoral activities of neutrophils in the mammary tissue.

Methods
Female BALB/cAnNTac mice at 7–8 weeks old were mated and bilateral ovariectomy was performed 2 days post-partum. At 24 h after forced-weaning of pups to induce mammary involution, post-partum female mice were injected with either E2V, or vehicle control on alternative days for 2-weeks. On 48 h post-weaning, treated female mice were inoculated subcutaneously with 4 T1-Luc2 cells into the 9th abdominal mammary gland. Age-matched nulliparous female was treated similarly. Animals were euthanized on day 14 post-tumour inoculation for analysis. To evaluate the short-term effect of estrogen, post-partum females were treated with only one dose of E2V on day 12 post-tumour inoculation.

Results
Estrogen treatment for 2-weeks reduces the number of blood LDN by more than 10-fold in tumour-bearing nulliparous and involuting mice, whilst it had no significant effect on blood HDN. The effect on tumour-bearing mice is associated with reduced number of mitotic neutrophils in the bone marrow and increased apoptosis in blood neutrophils. Since estrogen enhanced tumour growth in involuting mice, but not in nulliparous mice, we assessed the effect of estrogen on the gene expression associated with pro-tumoral activities of neutrophils. Whilst 48 h treatment with estrogen had no effect, 2-weeks treatment significantly increased the expression of Arg1, Il1b and Tgfb1 in both HDN and LDN of involuting mice. In contrast, estrogen increased the expression of Arg1 and Ccl5 in HDN and LDN of nulliparous mice.

Conclusions
Prolonged estrogenic stimulation in tumour-bearing mice markedly hampered tumour-associated increase of LDN plausibly by inhibiting their output from the bone marrow and by shortening their life span. Estrogen also alters the gene expression in neutrophils that is not seen in tumour-free mice. The results imply that estrogen may significantly influence the tumour-modulating activity of blood neutrophils.