bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA 3D structure prediction guided by independent folding of homologous sequences
Authors: Magnus Marcin , Kappel Kalli , Das Rhiju , Bujnicki Janusz
Published: October 2019

Background

The understanding of the importance of RNA has dramatically changed over recent years. As in the case of proteins, the function of an RNA molecule is encoded in its tertiary structure, which in turn is determined by the molecule's sequence. The prediction of tertiary structures of complex RNAs is still a challenging task.

Results

Using the observation that RNA sequences from the same RNA family fold into conserved structure, we test herein whether parallel modeling of RNA homologs can improve ab initio RNA structure prediction method. EvoClustRNA is a multi-step modeling process, in which homologous sequences for the target sequence are selected using the Rfam database. Subsequently, independent folding simulations using Rosetta FARFAR and SimRNA are carried out. The model of the target sequence is selected based on the most common structural arrangement of the common helical fragments. As a test, on two blind RNA-Puzzles challenges, EvoClustRNA predictions ranked as the first of all submissions for the L-glutamine riboswitch and as the second for the ZMP riboswitch. Moreover, through a benchmark of known structures, we discovered several cases in which particular homologs were unusually amenable to structure recovery in folding simulations compared to the single original target sequence.

Conclusion

This work, for the first time to our knowledge, demonstrates how important is the selection of the target sequence from an alignment of an RNA family for the success of RNA 3D structure prediction. These observations prompt investigations into a new direction of research for checking 3D structure “foldability” or “predictability” of related RNA sequences to obtain accurate predictions. To support new research in this area, we provide all relevant scripts in a documented and ready-to-use form. By exploring new ideas and identification of limitations of the current RNA 3D structure prediction methods, this work is bringing us closer to the near-native computational RNA 3D models.
Effects of Depression, Dementia and Delirium on Activities of Daily Living in Elderly Patients after Discharge
Authors: Weng Ching Fu , Lin Kun-Pei , Lu Feng-Ping , Chen Jen-Hau , Wen Chiung-Jung , Peng Jui-Hua , Tseng Ailun Heather , Chan Ding-Cheng
Published: October 2019

Background
The three geriatric conditions, depression, dementia and delirium (3D’s), are common among hospitalized older patients and often lead to impairments of activities of daily living. The aim of this study is to explore the impact of depression, dementia and delirium on activities of daily living (ADLs) during and after hospitalization.
Methods
A prospective cohort study was conducted between 2012 and 2013 in a tertiary medical center in Taiwan. Patients aged 65 years and older admitted to the geriatric ward were invited to this study. Geriatric Depression Scale Short Form, Mini-Mental State and Confusion Assessment Method were used to identify patients with depression, dementia and delirium on admission, respectively. Barthel Index (BI) was used to evaluate patients’ functional status on admission, at discharge, 30-day, 90-day and 180-day after discharge. Generalized Estimating Equation was used to calculate the associations between 3 D’s and BI.
Results
One-hundred-and-forty-nine patients were included in this study. Twenty-seven patients (18.1%) had depression, 37 (24.8%) had dementia, and 85 (57.0%) had delirium. There were significant lower BI scores in patients with dementia and delirium compared with those without up to 180 days after discharge, but no difference was seen in the depression group. In general, patients had delirium or dementia had worsening functional status, even though significant magnitude of improvements on BI scores after discharge.
Conclusions
Depression does not affect patients’ ADLs. On the other hand, dementia and delirium can persistently limit patients’ physical function. Future care should focus more on dementia and delirium to restore function.
Lack of Impact of Nil-Per-Os (NPO) Time on Goal-Directed Fluid Delivery in First Case versus Afternoon Case Starts: A Retrospective Cohort Study
Authors: Field R Ryan , Mai Tuan , Hanna Samouel , Harrington Brian , Calderon Michael-David , Rinehart Joseph
Published: October 2019

Background: Goal Directed Fluid Therapy(GDFT) represents an objective fluid replacement algorithm. The effect of provider variability remains a confounder. Overhydration worsens perioperative morbidity and mortality; therefore, the impact of the calculated NPO deficit prior to the operating room may reach harm.
Methods: A retrospective single-institution study analyzed patients at UC Irvine Medical Center main operating rooms from September 1, 2013 through September 1, 2015 receiving GDFT. The primary study question asked if GDFT suggested different fluid delivery after different NPO periods, while reducing inter-provider variability. We created two patient groups distinguished by 0715 surgical start time or start time after 1200. We analyzed fluid administration totals with either a 1:1 crystalloid to colloid ratio or a 3:1 ratio. We performed direct group-wise testing on total administered volume expressed as total ml, total ml/hr, and total ml/kg/hr between the first case start (AM) and afternoon case (PM) groups. A linear regression model included all baseline covariates that differed between groups as well as plausible confounding factors for differing fluid needs. Finally, we combined all patients from both groups, and created NPO time to total administered fluid scatterplots to assess the effect of patient-reported NPO time on fluid administration.
Results: Whether reported by total administered volume or net fluid volume, and whether we expressed the sum as ml, ml/hr, or ml/kg/hr, the AM group received more fluid on average than the PM group in all cases. In the general linear models, for all significant independent variables evaluated, AM vs PM case start did not reach significance in both cases at p=0.64 and p=0.19, respectively. In scatterplots of NPO time to fluid volumes, absolute adjusted and unadjusted R2 values are < 0.01 for each plot, indicating virtually non-existent correlations between uncorrected NPO time and fluid volumes measured.
Conclusions: This study showed NPO periods do not influence a patient’s volume status just prior to presentation to the operating room for surgical intervention. We hope this data will influence the practice of providers routinely replacing calculated NPO period volume deficit; particularly with those presenting with later surgical case start times.
Assessing the prevalence and risk factors of pre-diabetes among the community of Iganga Municipality, Uganda: A cross sectional study
Authors: Aramo Christine , Oyom Anthony Peter , Okello Emmanuel , Acam Victoria , Okiria John Charles , Mwambi Bashir , Oyet Caesar
Published: October 2019

Objective: The prevalence of pre-diabetes is increasing globally with more than 470 million people projected to develop pre-diabetes by 2030. In Africa, the average prevalence of pre-diabetes was estimated at 7.3% in 2015 and affected individual will develop type 2 diabetes mellitus within few decades. The aim of the study was to determine the prevalence of pre-diabetes and associated risk factors among residents of Iganga Municipality. A cross-sectional study was conducted among males and females aged 13-60 years. District health office provided updated household list from which sampling of the villages was performed based on probability proportionate to population. Consented participants were prepared for the study, allowing fasting for 8 to 10 hours before blood collection the next morning. Individuals with impaired fasting glucose, were subjected to OGTT. Results: 130 participants were enrolled, of which 98 were women. The mean age of the participants was 35 years. The prevalence of pre-diabetes was 3.8%. The proportion of impaired glucose tolerance was higher in current smokers (p = 0.01), obese participants (p = 0.002) and hypertensives (p <0.001). Prevalence of pre-diabetes is high in this community and is associated with current smoking, hypertension and high BMI.
Inflammatory blood biomarker response after controlled subconcussive head impacts: a pilot randomized controlled trial
Authors: Huibregtse Megan Elizabeth , Ejima Keisuke , Chen Zhongxue , Bevilacqua Zachary William , Koppineni Alekhya , Kalbfell Rachel M. , Kawata Keisuke
Published: October 2019

Background: Chronic neuroinflammation has been implicated as a possible contributing mechanism in the development and progression of chronic traumatic encephalopathy. This neurodegenerative condition has been associated with longterm, repetitive exposure to subconcussive head impacts, defined as head impacts that do not induce clinical signs or symptoms of concussion. However, there is a gap in knowledge surrounding the acute inflammatory response to subconcussive head impacts. The present study aimed to test our hypothesis that plasma levels of two proinflammatory markers (CCL11, CCL2) and one anti-inflammatory marker (IL-10) would be significantly elevated after 10 repetitions of controlled subconcussive head impacts. Methods: This randomized controlled trial included 39 healthy adult soccer players who were randomized into a heading (n=22) or kicking-control group (n=17). The heading group executed 10 headers with soccer balls projected at a speed of 25mph. The kicking-control group followed the same protocol with 10 kicks. Plasma samples were collected pre-, 0h post-, 2h post-, and 24h post-intervention. Samples were assayed for CCL11, CCL2, and IL-10, which are inflammatory markers that have shown to upregulate following traumatic brain injury. The longitudinal inflammatory marker data were analyzed using mixed-effect regression models. Results: There were no significant group differences in the changes of plasma CCL11, CCL2, or IL-10 levels at post-intervention time points as compared with pre-intervention baseline. However, within the heading group, there was a statistically significant interaction between time and years of soccer heading experience in plasma CCL11 levels at 24h post-intervention (2.0 pg/mL per a single year of soccer heading experience, 95% CI: 0.8, 3.1, p = 0.001). Conclusions: Ten soccer headings did not modulate the acute response in the three inflammatory marker levels compared against a kicking-control group. However, the acute CCL11 response may be influenced by the duration of prior exposure to subconcussive head impacts. Our data provide a precedent for future field studies that prospectively track head impact exposure and the time course of changes in circulating CCL11.
A Smart Glove Digital System Promotes Restoration of Upper Limb Motor Function and Enhances Cortical Neuroplastic Changes in Subacute Stroke Patients: A Randomized Controlled Trial
Authors: Lee Hwang-Jae , Chang Won Hyuk , Lee Ahee , Kim Hee-Goo , Ko Sung Hwa , Seong Hyun Yong , Shin Yong-Il , Kim Yun-Hee
Published: October 2019

Background: The sensor-based soft smart glove device is able to achieve multiple degree of freedom and complex motions with soft components. The purpose of this study was to examine the effects of RAPAEL ® Smart Glove digital training system on functional restoration of upper extremity and cortical neuroplastic changes in subacute stroke patients while provided in combined with conventional occupational therapy (OT).Methods: Fifty-two subacute stroke patients with upper extremity motor function deficit participated and 36 of them completed the interventional protocol (20 experimental group and 16 control group) . All participants were treated with conventional OT for 4 weeks, 5 times per week, 30 min per day. In addition, the experimental group received game-based digital hand motor training with the RAPAEL ® Smart Glove digital system for 4 weeks, 5 times per week, 30 min per day. The control group received additional OT for 30 min. The outcomes were assessed before intervention (T0), after 4 weeks of intervention (T1), and 4 weeks after cessation of intervention (T2) using Fugl-Meyer assessment (FMA) scale and Jebsen-Tayler hand function test (JTT). Oxygenated hemoglobin ( OxyHb ) levels over bilateral primary and secondary motor cortices during hand and wrist movement were measured using functional near infrared spectroscopy at T0 and T1.Results: All groups demonstrated improved upper extremity motor function for FMA total score and all subscores of JTT at T1, however, only experimental group showed further improvement at T2 ( p < 0.05). Also, the experimental group had significantly greater improvements upper extremity score of FMA scale and all subscores of JTT at T1 and T2 ( p < 0.05). Concentration of OxyHb over the ipsilesional sensorimotor cortex during wrist and hand movement was more increased in the experimental group than control group at T1 ( p < 0.05).Conclusion: This study demonstrated that training with the RAPAEL ® Smart Glove further improved upper extremity and hand motor function than conventional OT alone by enhancing ipsilesional motor cortical activity in subacute stroke patients.
Effect of ABO blood groups on response to warfarin
Authors: Zou Shan , Wu Lishan , Chen Zeliang , Li Hongxiao , Chen Hongjuan , Tan Xuerui , Yu Min
Published: October 2019

Background: Numerous studies have demonstrated that patients with non-O blood groups have higher risk for venous thromboembolism than those with O blood group. However, it has remained unknown about the effect of ABO blood groups on warfarin dose requirements in patients receiving anticoagulation in Chinese Han population. The study aimed to investigate the influence of ABO blood groups on warfarin dose requirements in Chinese Han population.
Methods: A retrospective study was conducted in the First Affiliated Hospital of Shantou University Medical College in Southern China. Three hundreds and 58 patients with confirmed diagnosis of deep venous thromboembolism and atrial fibrillation were included. Frequency of blood groups and warfarin dose requirements were determined.
Results: Of 358 patients with deep venous thromboembolism and atrial fibrillation, 111 patients had blood group A (31.01%), 104 patinets had blood group B (29.05%), 20 patients had blood group AB (5.59%), and 123 patients had blood group O (34.36%). The patients with O blood group had a lower warfarin dose requirements compared with those with A, B and AB blood group.
Conclusion: Our study showed that patients with non-O blood groups require higher doses of warfarin.
Management of button batteries in the upper gastrointestinal tract of children
Authors: gao yan , wang jin , ma jing , Gao Yingqin , Zhang Tiesong , Lei Puping , Xiong Xin
Published: October 2019

Background: To analyze the lodging locations of ingested button batteries in the upper gastrointestinal tract of children, common complications and treatment effects. Methods: The clinical data of 14 children with ingested button batteries lodged in the upper gastrointestinal tract were analyzed in our hospital between 2017 and 2019. Results: Among 10 children with ingested button batteries lodged in the first stenosis of esophagus, 9 were cured and 1 suffered from esophagotracheal fistula 12 days after removal. One child with the ingested button battery lodged in the second stenosis of esophagus was dead due to intercurrent aortoesophageal fistula 13 days after removal. Two cases had ingested button batteries lodged in the third stenosis of esophagus, and were cured after removal. The ingested button battery in 1 case was lodged in the gastrointestinal tract, and discharged spontaneously 1 day after hospital admission. Conclusions: Ingested button batteries are mainly lodged in the esophageal stenoses. Longer retention time could induce esophageal fistula. The ingested button battery in the gastrointestinal tract can discharge spontaneously.
Reactivity and reproducibility of accelerometer-based sedentary behavior and physical activity in two measurement periods: Results of a feasibility randomized-controlled study
Authors: Ullrich Antje , Baumann Sophie , Voigt Lisa , John Ulrich , Ulbricht Sabina
Published: October 2019

Background: The aims of the study were to investigate measurement reactivity in sedentary behavior (SB), physical activity (PA), and accelerometer wear time in two measurement periods, to examine the reproducibility of these outcomes and to quantify measurement reactivity as a confounder for the reproducibility of SB and PA data.Methods: A total of 136 participants (65% women, mean age = 54.6 years, study period 02/2015 to 08/2016) received 7-day accelerometry at baseline and after 12 months. Latent growth models were used to identify measurement reactivity in each period. Intraclass correlations (ICC) were calculated to examine the reproducibility using two-level mixed-effects linear regression analyses. Results: At both measurements periods, participants increased time spent in SB (b=2.3 min/d; b=3.8 min/d), reduced time spent in light PA (b=2.0 min/day; b=3.3 min/d), but did not change moderate-to-vigorous PA. Participants reduced accelerometer wear time (b=4.6 min/d) only at baseline. The ICC coefficients ranged from 0.42 (95% CI=0.29-0.57) for accelerometer wear time to 0.70 (95% CI=0.61-0.78) for moderate-to-vigorous PA. In none of the regression models, a reactivity indicator was identified as a confounder for the reproducibility of SB and PA data.Conclusions: The results show that measurement reactivity differentially influences SB and PA in two measurement periods. Although 7-day accelerometry seems to be a reproducible measure of SB and PA, our findings highlight the importance of accelerometer wear time as a crucial confounder when using accelerometry in monitoring SB and PA, planning interventions, and analyzing SB and PA data.Clinical trial registration number: NCT02990039 (retrospectively registered); December 12, 2016
Effect of gga-miR-155 on Cell Proliferation, Apoptosis and invasion of Marek’s disease Virus (MDV) transformed cell line MSB1 by targeting RORA
Authors: Ding Ke , Yu Zuhua , Yu Chuan , Jia Yanyan , He Lei , Liao Chengshui , Li Jing , Zhang Chunjie , Li Yingju , Wu Tingcai , Cheng Xiangchao , Zhou Zhiyu , Yu Zuling
Published: October 2019

Background: Marek's disease (MD) is an avian lymphoproliferative neoplasm caused by the oncogenic Marek's disease virus (MDV). MicroRNAs (miRNAs) act as oncogenes or tumor suppressors in most cancers. The gga-miR-155 is downregulated in the MDV-infected chicken tissues or lymphocyte lines, although its exact role in tumorigenesis remains unclear. The aim of this study was to analyze the effects of gga-miR-155 on the proliferation, apoptosis and invasiveness of an MDV-transformed lymphocyte line MSB1 and elucidate the underlying mechanisms. Results: The expression level of gga-miR-155 was manipulated in MSB1 cells using specific mimics and inhibitors. While overexpression of gga-miR-155 increased proliferation, decreased the proportion of G1 phase cells relative to that in S and G2 phases, reduced apoptosis rates and increased invasiveness. However, its downregulation had the opposite effects. Furthermore, gga-miR-155 directly targetedthe RORA gene and downregulated its expression in the MSB1 cells.Conclusion: The gga-miR-155 promotes the proliferation and invasiveness of the MDV-transformed lymphocyte line MSB1 and inhibits apoptosis by targeting the RORA gene.
Trends of severe acute malnutrition morbidity and mortality (2014-2017), Bale Zone, Oromia Region, Ethiopia, 2018
Authors: Badeso Mohammed Hasen , Ferede Henok Asefa , Bogale Naod Berhanu , Kalil Falaho Sani
Published: October 2019

Background Malnutrition is a serious disease and remains an important public health problem in many developing countries including Ethiopia. Malnutrition is one of the diseases under the surveillance system which is reported weekly and monthly. In the Bale zone, malnutrition is one of the major public health problems. Therefore, this trend analysis of severe acute malnutrition was to describe the magnitude, trends, disease outcome and geographical distribution of the severe acute malnutrition in Bale Zone from 2014-2017.Methods A descriptive cross-sectional study was conducted on April 2018. Data was extracted from Bale zone monthly malnutrition report database and checked for completeness and consistency then four years’ trends of severe acute malnutrition were analyzed. The prevalence and trend of severe acute malnutrition by Woreda, year and age were analyzed using Microsoft office excel and SPSS version 20 then summarized using text, table, and figure.Result A total of 37,678 severe acute malnutrition cases registered over four years (2014-2017). Of these, 31,642(84%) cured, 52(0.14%) died, 641(1.7%) defaulters, 66(0.18%) non-respondents. Among registered cases, 98.2% are 6-59months age groups. The average annual prevalence of severe acute malnutrition high among under-five children was 3.3%. Prevalence rate per 1000 population of severe acute malnutrition in 2014, 2015,2016 and 2017 are 3.6, 4.5, 7.5 and 4.7 respectively and death rate are 0.21%, 0.26%, 0.1% and 0.08% respectively. Among the Woreda, the highest prevalence at Delomena (2.45%) and lowest at Sinana woreda (0.1%). The death rate is high among 6-59months age groups (0.13%) and followed by less than 6months age group (0.008%).Conclusion Cases of severe acute malnutrition increased during the year 2014 to 2016 then decreased during 2017. The prevalence of severe acute malnutrition high in under-five age groups children at Bale zone during the study period and Delomena Woreda has the highest average annual prevalence of severe acute malnutrition. We recommend further research on why some district has a high prevalence of severe acute malnutrition.
Suprapatellar versus infrapatellar approaches in the treatment of tibia intramedullary nailing: A retrospective cohort study
Authors: Cui Yiliang , Hua Xingyi , Schmidutz Florian , Zhou Jian , Yin Zongsheng , Yan Shuang G
Published: October 2019

Background: Tibial shaft fractures are routinely managed with intramedullary nailing (IMN). An increasingly accepted technique is the suprapatellar (SP) approach. The purpose of this study was to compare the clinical and functional outcomes of knee joint after tibia IMN through an suprapatellar (SP) or traditional infrapatellar (IP) approach. Methods: Retrospective analysis was performed in patients with tibial shaft fractures that were treated with tibia IMN through a SP or IP approach (1/2014-11/2016). The clinical and functional outcomes of knee joint were assessed with the Hospital for Special Surgery (HSS) Knee Score. Further evaluation included the operation time, intraoperative blood loss. Results: A total of 50 patients/fractures (26 IP and 24 SP) with a follow-up for a minimum of 15 months were evaluated. All fractures were OTA 42. No significant differences were found between the two groups in age, gender, side of fractures, operation time, intra-operative blood loss, and follow-up time. No significant difference was seen in HSS score ( P = 0.62) between them. Analysis of all the HSS components scores revealed no significant differences between them concerning the pain ( P = 0.57), the stand and walk ( P = 0.54), the need for walking stick ( P = 0.60) and extension lag ( P = 0.60). The other HSS components showed full scores (IP 10 vs. SP 10) in both approaches, including muscle force, flexion deformity and stability components. The range of motion (ROM) component score was superior in the IP group ( P = 0.04) suggesting a higher ROM. Conclusions: The SP and IP approaches can get equivalent knee functional outcomes in the treatment of tibial shaft fracture concerning the overall HSS knee score. However, for the HSS component, the IP approach was superior to SP approach regarding the ROM.
Utility of Magnetic Resonance Imaging in determining treatment response and local recurrence in Nasopharyngeal Carcinoma treated curatively
Authors: Meng Katherine , Tey Jeremy , Ho Francis , Asim Hira , Cheo Timothy
Published: October 2019

Background: To determine the optimal timing of the first Magnetic Resonance Imaging (MRI) scan after curative-intent radiotherapy (RT) for nasopharyngeal carcinoma (NPC), and evaluate the role of MRI in surveillance for locoregional recurrence (LRR).

Methods: Patients with non-metastatic NPC treated radically with at least one post-treatment MRI (ptMRI) were included for analysis. ptMRI reports were retrospectively reviewed and categorised as complete response (CR), partial response/residual disease (PR) or indeterminate (ID). Patients with LRR were assessed to determine if initial detection was by MRI or clinical means. Univariable and multivariable Cox proportional hazard regression analysis were performed to identify independent factors associated with CR on ptMRIs.

Results: Between 2013 and 2017, 262 eligible patients were analysed, all treated with Intensity Modulated Radiotherapy (IMRT). Median time from end of RT to the first ptMRI was 93 days (range 32-346). Of the first ptMRIs, 88 (33.2%) were CR, 133 (50.2%) ID, and 44 (16.6%) PR. A second ptMRI was done for 104 (78.2%) of 133 patients with ID status. In this group, 77 (57.9%) of the subsequent MRI were determined to be CR, 21(15.8%) remained ID and 6 (4.5%) PR. T1 tumour stage and AJCC stage I were associated with increased CR rates on first ptMRI on multivariable analysis. ID status was more likely at 75-105 days (3 months +/- 15 days) vs 106-135 days (4 months +/- 15 days) post RT (OR 2.13, 95% CI 1.16-4.12, p=0.024). LRR developed in 27 (10.1%) patients; 20 (74.1%) was initially detected through MRI, 3 (11.1%) by nasoendoscopy and 2 (7.4%) by PET-CT.

Conclusion: MRI is useful for detecting local recurrence or persistent disease after curative-intent treatment. Most patients will need more than one ptMRI to arrive at a definitive status. The rate of ID ptMRI may be reduced by delaying the first scan to around 4 months post RT.
Downregulated ZNF132 Predicts Unfavorable Outcomes in Breast Cancer via Hypermethylation Modification
Authors: Liu Zhao , Liu Jiaxin , Xue Man , Zhang Weifan , Zhao Xinhui , Xia Peng
Published: October 2019

Background: Methylation modification of tumor suppressor gene is one of the most critical mechanisms in human breast cancer (BC). Some biomarkers, including HER2, ER and PR, have been used in clinical practice, however, the effective was limited in terms of high recurrence and mortality rate. Thus, a better diagnostic and therapeutic target for BC is urgent. To date, no study provide information on the status of ZNF132 in BC or analyze diagnosis and prognostic significance of ZNF132 in BC. Methods: In the present study, we investigated the expression and clinical signifcance of ZNF132 by TCGA database and clinical samples analysis. Besides, a further exploration was performed to assess the molecular mechanisms of ZNF132 using the multiple bioinformatic tools. Importantly, a MSP assay was executed to confirm the epigenetic alteration of ZNF132. Results: Our results showed that the mRNA expression of ZNF132 was significantly downregulated in BC tissues, the consistent results was obtained by immunohistochemistry assessment. Importantly, survial analysis revealed that the lower expression of ZNF132 was remarkably correlated to Relapse Free Survival (RFS), but not Overall Survival (OS). Besides, the ROC curve confirmed ZNF132 had powerful sensitivity and specificity to distinguish between BC and adjacent normal tissues. Finally, MSP analysis demonstrated that ZNF132 was hypermethylated in BC tissues. Interestingly, ZNF132 methylation level was negatively correlated with its gene expression. Conclusions: Our results revealed that hypermethylation of ZNF132 contributed to its downregulated expression and could be identified as a new diagnostic and prognostic marker in BC.
Petri net Modeling and Property Analysis of C3 plant Photosynthesis and Photorespiration
Authors: Singh Gajendra Pratap , Jha Madhuri
Published: October 2019

Metabolic pathway - Modeling and Analysis, is the emerging research area in Biochemistry over the past few years.C3plants are the best carbohydrate producers and also are the most common plants found in the nature. These plants are very much efficient in photosynthesis in cool and wet climate while, in very hot climatic condition it undergoes photorespiration process. In this paper we model the process of making food by C3 plants to study the behavior in different climate conditions.
Efficacy of Bimin Decoction on patients with perennial allergic rhinitis: an open-label non-inferiority randomized controlled trial
Authors: Zhao Jingyi , Yan Xinyu , Gai Jianqing , Han Jinshuai , Zhang Hong , Luo Hui , Huang Shaoting , Wang Junge
Published: October 2019

Abstract
Background: Allergic rhinitis (AR) is a common allergic disease which affects people worldwide and traditional Chinese medicine is getting popular among AR patients for definite clinical effect and less adverse reactions. Lung qi deficiency and cold syndrome (LQDCS) is a frequent type of AR, and Chinese herbal medicine Bimin Decoction (BMD) was generated for AR patients with LQDCS. This study aimed to compare the clinical efficacy of BMD for AR patients with LQDCS to conventional medicine loratadine and fluticasone nasal spray.
Methods/Design: The study was designed as an open-label, non-inferiority, randomized controlled trial. A total of 108 AR patients with LQDCS aged 19 to 60 were 1:1 randomly allocated to BMD group and control group by central computer system in Beijing Hospital of Traditional Chinese Medicine from January 2017 to April 2018. 98 completed the study (n=51; n=47). Patients in BMD group received Bimin Decoction while the control group received fluticasone nasal spray and loratadine tablets for a 4-week treatment. The primary outcome was change of the Total Nasal Symptom Score (TNSS) at baseline and the end of treatment. Alterations in Rhinoconjunctivitis Quality Life quality Questionnaire (RQLQ), nasal resistance (NR) and acoustic rhinometry parameters were second outcomes. Any side effect of treatment was observed and recorded.
Results: After the 4-week treatment the TNSS total score was significantly reduced in both groups from baseline ( P < 0.05), no significant between-groups differences were observed for the changes of TNSS scores [-0.298 (95% CI -0.640 to 0.140)], which was within the defined non-inferiority margin. RQLQ in both groups decreased significantly ( P < 0.001) from baseline and more obvious reduction in BMD group was observed ( P < 0.001). There was no significant difference in the nasal resistance, the nasal volume and the nasal minimum cross-sectional area after treatment between groups ( P > 0.05).
Conclusions: These findings indicated that BMD helps relieve PAR symptoms and improve rhinitis-related life quality. Our study indicated that BMD is non-inferior to loratadine tablets and fluticasone nasal spray for AR patients with LQDCS.
Trial registration: Chinese Clinical Trial Registry, ChiCTR-INR-16010063. Registered on 2 December, 2016
Keywords: Perennial allergic rhinitis, Chinese traditional medicine, Randomized controlled trial, Clinical efficacy
Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts
Authors: Burkhardt Alyssa Kay , Childs Kevin L. , Wang Jie , Ramon Marina L. , Martin Frank N.
Published: October 2019

Background: Macrophomina phaseolina is a fungal plant pathogen with a broad host range, but one genotype was shown to exhibit host preference/specificity on strawberry. This pathogen lacked a high-quality genome assembly and annotation, and little was known about genomic differences among isolates from different hosts.

Results: We used PacBio sequencing and Hi-C scaffolding to provide nearly complete genome assemblies for M. phaseolina isolates representing the strawberry-specific genotype and another genotype recovered from alfalfa. The strawberry isolate had 59 contigs/scaffolds with an N50 of 4.3 Mb. The isolate from alfalfa had an N50 of 5.0 Mb and 14 nuclear contigs with half including telomeres. Both genomes were annotated with MAKER using transcript evidence generated in this study with over 13,000 protein-coding genes predicted. Unique groups of genes for each isolate were identified when compared to closely related fungal species. Structural comparisons between the isolates reveal large-scale rearrangements including chromosomal inversions and translocations. To include isolates representing a range of pathogen genotypes, an additional 30 isolates were sequenced with Illumina, assembled, and compared to the strawberry genotype assembly. Within the limits of comparing Illumina and PacBio assemblies, no conserved structural rearrangements were identified among the isolates from the strawberry genotype compared to those from other hosts, but some candidate genes were identified that were largely present in isolates of the strawberry genotype and absent in other genotypes.

Conclusions: High-quality reference genomes of M. phaseolina have allowed for the identification of structural changes associated with a genotype that has a host preference toward strawberry and will enable future comparative genomics studies. Having more complete assemblies allows for structural rearrangements to be more fully assessed and ensures a greater representation of all the genes. Work with Illumina data from additional isolates suggests that some genes are predominately present in isolates of the strawberry genotype, but additional work is needed to confirm the role of these genes in pathogenesis. Additional work is also needed to complete the scaffolding of smaller contigs identified in the strawberry genotype assembly and to determine if unique genes in the strawberry genotype play a role in pathogenicity.
Symbiotic bacteria motivate the foraging decision and promote fecundity and survival of Bactrocera dorsalis (Diptera: Tephritidae)
Authors: Akami Mazarin , Ren Xue-Ming , Qi Xuewei , Mansour Abdelaziz , Gao Bingli , Cao Shuai , Niu Chang-Ying
Published: October 2019

Background The gut bacteria of tephritid fruit flies play prominent roles in nutrition, reproduction, maintenance and ecological adaptations of the host. Here, we adopted an approach based on direct observation of symbiotic or axenic flies feeding on dishes seeded with drops of full diet (containing all amino acids) or full diet supplemented with bacteria at similar concentrations to explore the effects of intestinal bacteria on foraging decision and fitness of Bactrocera dorsalis. Results The results show that intestinal probiotics elicit beneficial foraging decision and enhance the female reproduction fitness and survival of B. dorsalis (symbiotic and axenic), yet preferences for probiotic diets were significantly higher in axenic flies to which they responded faster compared to full diet. Moreover, females fed diet supplemented with Pantoea dispersa and Enterobacter cloacae laid more eggs but had shorter lifespan while female fed Enterococcus faecalis and Klebsiella oxytoca enriched diets lived longer but had lower fecundity compared to the positive control. Conversely, flies fed sugar diet (negative control) were not able to produce eggs, but lived longer than those from the positive control. Conclusions These results suggest that intestinal bacteria can drive the foraging decision in a way which promotes the reproduction and survival of B. dorsalis. Our data highlight the potentials of gut bacterial isolates to control the foraging behavior of the fly and c empower the sterile insect technique (SIT) program through the mass rearing.
Comparison of GeneXpert and Line Probe Assay for Detection of Mycobacterium tuberculosis and Rifampicin-Mono resistance at the National Tuberculosis Reference Laboratory, Kenya
Authors: Aricha S.A. , King'wara Leonard , Mwirigi N.W. , Chaba Linda , Kiptai T. , Wahogo J. , Otwabe J.S , Onyango P.O. , Karanja Muthoni , Ayieko C. , Matu S.W.
Published: October 2019

Background: The dual challenge of low diagnostic sensitivity of microscopy test and technical challenge of performing a TB culture test poses a problem for case detection and initiation of Tuberculosis (TB) second-line treatment. There is thus need for a rapid, reliable and easily accessible assay. This comparative analysis was performed to assess diagnostic performance characteristics of GeneXpert MTB/RIF and Line Probe Assay (LPA)
Methods : 329 sputum samples of patients across the 47 counties in Kenya suspected to have drug resistant TB were picked and subjected to GeneXpert, LPA and Culture MGIT at the National TB Reference Laboratory. Sensitivity, specificity and predictive values were then determined to assess the performance characteristics of the various assays.
Results: Against culture MGIT as the gold standard for TB diagnosis, GeneXpert had a sensitivity, specificity, positive predictive value, and negative predictive value of 78.5%, 64.9%, 59.4 % and 82.2% respectively while LPA had 98.4%, 66.0 %, 65.4% and 98.4%. For diagnosis of rifampicin mono-resistance GeneXpert had a moderate agreement (Kappa 0.59, P<0.01) (sensitivity 62.50%, specificity 96.50 %) while LPA that had almost perfect agreement (Kappa=0.89, p<0.01) with a (sensitivity 90.0% and specificity 99.1%).
Conclusion : LPA has a better performance characteristic to GeneXpert and an alternative to culture with regards to detection of RIF’s mono-resistance.
Keywords : LPA, GeneXpert, Sensitivity, Specificity, Drug-resistant TB
Runoff pH Influences Nutrient Removal Efficacy of Floating Treatment Wetland Systems
Authors: Garcia Chance Lauren M. , Albano Joseph P. , Lee Cindy M. , Wolfe Staci M. , White Sarah A.
Published: October 2019

Floating treatment wetlands (FTWs), a modified constructed wetland technology, can be deployed in ponds for the treatment of nursery and greenhouse irrigation runoff. The pH of nursery and greenhouse operation irrigation water varies from 3.3 to 10.4 across the United States. Water flow rate, plant species selection, and variable nutrient inputs influence the remediation efficacy of FTWs and may interact with the pH of inflow water to change nutrient remediation dynamics. Therefore, an experiment was designed to quantify the effect of pH on the growth and nutrient uptake capacity of three macrophyte species using a mesocosm FTW system. ‘Rising Sun’ japanese iris (Iris ensata), bushy bluestem (Andropogon glomeratus), and maidencane (Panicum hemitomon) were grown for two 6-week periods and exposed to five pH treatment levels representing the range of nursery and greenhouse irrigation runoff, 4.5, 5.5, 6.5, 7.2, and 8.5, for a total of 15 plant and pH combinations. Water was treated with either hydrochloric acid to decrease the pH or sodium hydroxide to increase the pH. The pH-adjusted solutions were mixed with 12 mg·L−1 nitrogen (N) and 6 mg·L−1 phosphorus (P) fertilizer (64.8 g·m−3 N and 32.4 g·m−3 P). Differences in pH impacted both N and P removal from the FTW systems for two of the three species studied, maidencane and bushy bluestem. Higher pH treatments reduced nutrient removal efficacy, but plants were still capable of consistently removing nutrients across all pH treatments. Conversely, ‘Rising Sun’ japanese iris maintained similar remediation efficacies and removal rates across all pH treatments for both N and P, possibly due to the ability to acidify its rhizosphere and modify the pH of the system. Average N and P loads were reduced by 47.3 g·m−3 N (70%) and 16.6 g·m−3 P (56%). ‘Rising Sun’ japanese iris is a promising plant for use in highly variable conditions when the pH of irrigation runoff is outside the typical range (5.5–7.5). Results from model simulations poorly predict the nutrient availability of P and ammonium in effluent, most likely due to the inability to determine plant and biological contributions to the system, such as N-fixing bacteria.
Immunohistochemical Subtype and Parameters of International Prognostic Index in the New Prognostic Model of Diffuse Large B-Cell Lymphoma
Authors: Samarina Svetlana Valer'evna , Luchinin A.S. , Minaeva N.V. , Paramonov I.V. , D'yakonov D.A. , Vaneeva E.V. , Rosin V.A. , Gritsaev S.V.
Published: October 2019

Aim. To develop an integrated prognostic model of diffuse large B-cell lymphoma (DLBCL) on the basis of immunohis-tochemical tumor subtype and parameters of International Prognostic Index (IPI). Materials & Methods. Out of 104 DLBCL patients in the data base 81 (77.9 %) met the eligibility criteria. Median age was 58 years (range 23-83). All patients were treated with R-СНОР. The creation of overall survival (OS) prognostic model for DLBCL patients was based on machine learning with classification and regression trees. OS was analyzed using Kaplan-Meier method. Survival curves were compared by means of log rank test and hazard ratio (HR). Any test was considered significant if two-sided level of p < 0.05 was reached. Results. Following the developed model three groups of patients were identified: the 1st group of low risk (the combination of low, intermediate-low, and intermediate-high risks according to IPI and GCB subtype); the 2nd group of intermediate risk (the combination of low, intermediate-low, and intermediate-high risks according to IPI and non-GCB subtype); the 3d group of high risk (irrespective of subtype). In the group of low risk (n = 26) 2-year OS during the monitoring period was 100 %. In the group of intermediate risk (n = 34) median OS was not reached, 2-year OS was 74 %, and expected 5-year OS was 68 %. In the group of high risk (n = 21) median OS was 25 months, 2-year OS was 46 %, and expected 5-year OS was 37 % (log rank p < 0.0001). HR calculated for the high-risk group compared with the low- and intermediate-risk groups was 5.1 (95% CI 2.112.1; p = 0.0003). Conclusion. A new integrated system of DLBCL prognosis is suggested which includes IPI risk parameters and immunohistochemical subtype based on Hans algorithm. This prognostic system can be used in clinical practice for DLBCL patient stratification and risk-adapted therapy.
Expression of Rice Metallothionein Isoforms in Escherichia coli Enhances the Accumulation of Trivalent and Hexavalent Chromium
Authors: Shahpiri Azar , Rahimi Amir Mohammad
Published: October 2019

Introduction: Metallothioneins (MTs) are members of a family of low molecular weight and cysteine-rich proteins that are involved in heavy metal homeostasis and detoxification in living organisms. Plants have multiple MT types that are generally divided into four subgroups according to the arrangement of Cys residues.  Methods: In the present study the E. coli cells which heterologously express four different rice MT (OsMT) isoforms were analyzed for the accumulation of two forms of chromium, Cr3+ and Cr6+.  Results: The results show that the transgenic bacteria were more tolerant than control cells when they were grown up in the medium comprising Cr(NO3)3.9H2O or Na2CrO4. The cells expressing OsMT1, OsMT2, OsMT3 and OsMT4 give rise to 6.5-, 2.7-, 5.5- and 2.1-fold improvements on the accumulation capacity for Cr3+ and 9-, 3-, 5- and 3- fold Cr6+ respectively compared with comparison to the control strain. Furthermore, the purified recombinant GST-OsMTs were tested for their binding ability to Cr+3 and Cr+6 in vitro.  Discussion: The data show that the recombinant GST-OsMT1 and GST-OsMT2 were able to bind both Cr3+ and Cr6+, in vitro. However, their binding strength was low with respect to previous tested divalent ions like Cd2+.
NMAAP1 Maintains M1 Phenotype in Macrophages Through Binding to IP3R and Activating Calcium-related Signaling Pathways
Authors: Liu Qihui , Zhu Pei , Liu Shanshan , Tang Mengyan , Wang Yuanxin , Tian Yuan , Jin Zheng , Li Dong , Yan Dongmei
Published: October 2019

Background:

NMAAP1 plays a role in regulating macrophage differentiation to the M1 type and exerting antitumoral functions. It is not clear what role and mechanism NMAAP1 does play in the reversal of macrophages from M1 to M2.

Methods:

We detected the typing of macrophages with high or low expression of NMAAP1 by QPCR and ELISA, and detected the colocalization of NMAAP1 and endogenous IP3R by laser confocal microscopy, and detected the protein expression in cells by Western-blotting.

Methods:

Our study found that knockdown NMAAP1 in RAW264.7 cells induced macrophage polarization to the M2 type and up-regulation of NMAAP1 in RAW264.7 cells maintain M1 Phenotype even in the presence of IL-4, a stronger inducer of the M2 type. Additionally, Coimmunoprecipitation revealed a protein-protein interaction between NMAAP1 and IP3R and then activates key molecules in the PKC-dependent Raf/MEK/ERK and Ca2+/CaM/CaMKII signaling pathways. Activation of PKC (Thr638/641), ERK1/2 (Thr202/Tyr204) and CaMKII (Thr286) is involved in the regulation of cell differentiation.

Conclusion:

NMAAP1 interacts with IP3R, which in turn activates the PKC-dependent Raf/MEK/ERK and Ca2+/CaM/CaMKII signaling pathways. These results provide a new explanation of the mechanism underlying M1 differentiation.
Identification of Antibacterial Molecule(s) from Animals Living in Polluted Environments
Authors: Winnie Foo Y.M. , Siddiqui Ruqaiyyah , Sagathevan Kuppusamy , Khan Naveed A.
Published: October 2019

Background:

Snakes feed on germ-infested rodents, while water monitor lizards thrive on
rotten matter in unhygienic conditions. We hypothesize that such creatures survive the assault of superbugs
and are able to fend off disease by producing antimicrobial substances. In this study, we investigated
the potential antibacterial activity of sera/lysates of animals living in polluted environments.

Methods:

Snake (Reticulatus malayanus), rats (Rattus rattus), water monitor lizard (Varanus salvator),
frog (Lithobates catesbeianus), fish (Oreochromis mossambicus), chicken (Gallus gallus domesticus),
and pigeon (Columba livia) were dissected and their organ lysates/sera were collected. Crude extracts
were tested for bactericidal effects against neuropathogenic E. coli K1, methicillin-resistant Staphylococcus
aureus (MRSA), Streptococcus pyogenes, Pseudomonas aeruginosa, Bacillus cereus and
Klebsiella pneumoniae. To determine whether lysates/sera protect human cells against bacterialmediated
damage, cytotoxicity assays were performed by measuring lactate dehydrogenase release as
an indicator of cell death. Lysates/sera were partially characterized using heat-treatment and pronasetreatment
and peptide sequences were determined using the Liquid Chromatography Mass Spectrometry
(LC-MS).

Results:

Snake and water monitor lizard sera exhibited potent broad-spectrum bactericidal effects
against all bacteria tested. Heat inactivation and pronase-treatment inhibited bactericidal effects indicating
that activity is heat-labile and pronase-sensitive suggesting that active molecules are proteinaceous
in nature. LCMS analyses revealed the molecular identities of peptides.

Conclusion:

The results revealed that python that feeds on germ-infested rodents and water monitor
lizards that feed on rotten organic waste possess antibacterial activity in a heat-sensitive manner and
several peptides were identified. We hope that the discovery of antibacterial activity in the sera of animals
living in polluted environments will stimulate research in finding antibacterial agents from unusual
sources as this has the potential for the development of novel strategies in the control of infectious
diseases.