bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of two commercial recirculated aquacultural systems and their microbial potential in plant disease suppression
Authors: Khalil Sammar , Panda Preeti , Ghadamgahi Farideh , Rosberg AnnaKarin , Vetukuri Ramesh R 
Published: July 2021

Abstract
Background
Aquaponics are food production systems advocated for food security and health. Their sustainability from a nutritional and plant health perspective is, however, a significant challenge. Recirculated aquaculture systems (RAS) form a major part of aquaponic systems, but knowledge about their microbial potential to benefit plant growth and plant health is limited. The current study tested if the diversity and function of microbial communities in two commercial RAS were specific to the fish species used (Tilapia or Clarias) and sampling site (fish tanks and wastewaters), and whether they confer benefits to plants and have in vitro antagonistic potential towards plant pathogens.

Results
Microbial diversity and composition was found to be dependent on fish species and sample site. The Tilapia RAS hosted higher bacterial diversity than the Clarias RAS; but the later hosted higher fungal diversity. Both Tilapia and Clarias RAS hosted bacterial and fungal communities that promoted plant growth, inhibited plant pathogens and encouraged biodegradation. The production of extracellular enzymes, related to nutrient availability and pathogen control, by bacterial strains isolated from the Tilapia and Clarias systems, makes them a promising tool in aquaponics and in their system design.

Conclusions
This study explored the microbial diversity and potential of the commercial RAS with either Tilapia or Clarias as a tool to benefit the aquaponic system with respect to plant growth promotion and control of plant diseases.
Epidemiology of SARS-CoV2 in Qatar’s primary care population aged 10 years and above
Authors: Syed Mohamed Ahmed , Al Nuaimi Ahmed Sameer , A/Qotba Hamda Abdulla , Nasrallah Gheyath K. , Althani Asmaa A. , Yassine Hadi M. , Zainel Abduljaleel Abdullatif , Khudadad Hanan , Marji Tamara , Veettil Shajitha Thekke , Al-Jighefee Hadeel T. , Younes Salma , Shurrab Farah , Al-Sadeq Duaa W. , AlFehaidi Al Anoud Saleh , Yfakhroo Ameena Ibrahim , AlMesaifri Meshal Abdulla , Al Mujalli Hanan , Al Abdulla Samya Ahmad , Al Kuwari Mohamed Ghaith , Azad Faruk Mohammed , Al Malki Badria Ali Mohamed , Abdulmalik Mariam Ali 
Published: July 2021

Abstract
Background
There is an urgent need to elucidate the epidemiology of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) and characterize its potential impact. Investing in characterising the SARS-CoV2 will help plan and improve the response to the pandemic. Furthermore, it will help identify the most efficient ways of managing the pandemic, avoiding public health policies and interventions that may be unduly restrictive of normal activity or unnecessarily costly. This paper describes the design and reports findings of a population based epidemiological study undertaken to characterise SARS-CoV2 in Qatar using limited resources in a timely manner.

Methods
Asymptomatic individuals ≥10 years registered with Qatar’s publicly funded primary health provider were eligible. A stratified random sampling technique was utilized to identify the study sample. Participants were invited to an appointment where they completed a questionnaire and provided samples for polymerase chain reaction and Immunoglobulin M and G immunoassay tests. Data collected were analyzed to calculate point and period prevalence by sociodemographic, lifestyle and clinical characteristics.

Results
Of 18,918 individuals invited for the study, 2084 participated (response rate 10.8%). The overall point prevalence and period prevalence were estimated to be 1.6% (95% CI 1.1–2.2) and 14.6% (95% CI 13.1–16.2) respectively. Period prevalence of SARS-CoV2 infection was not considerably different across age groups (9.7–19.8%). It was higher in males compared to females (16.2 and 12.7% respectively). A significant variation was observed by nationality (7.1 to 22.2%) and municipalities (6.9–35.3%).

Conclusions
The study provides an example of a methodologically robust approach that can be undertaken in a timely manner with limited resources. It reports much-needed epidemiological data about the spread of SARS-CoV2. Given the low prevalence rates, majority of the population in Qatar remains susceptible. Enhanced surveillance must continue to be in place, particularly due to the large number of asymptomatic cases observed. Robust contact tracing and social distancing measures are key to prevent future outbreaks.
Immune cell profiling and antibody responses in patients with COVID-19
Authors: Rezaei Mitra , Mahmoudi Shima , Mortaz Esmaeil , Marjani Majid 
Published: July 2021

Abstract
Background
Although there are a growing number of studies on evaluating lymphocyte subset counts as prognostic factors for COVID-19 disease severity, the lymphocyte subsets’ analyses of both IgM and IgG responders and non-responders during the periods after onset of symptoms, have not been conducted yet. So, this study aimed to evaluate immune cell profiling of COVID-19 patients with and without antibody responses.

Methods
In this cross-sectional study, the levels of peripheral lymphocyte subsets were measured using flow cytometry in 53 patients with positive SARS-CoV-2 RT-PCR, for whom antibody testing of COVID-19 was performed.

Results
The white blood cell, neutrophil, and lymphocyte counts consistently decreased in the IgM and IgG non-responder group, while the differences in the median value between the two study groups were found to be statistically significant only in terms of neutrophil counts (P = 0.024 for IgM response and p-value = 0.046 for IgG response, respectively). Moreover, the level of neutrophil-to-lymphocyte ratio was observed to be significantly lower in the IgM or IgG non-responder group compared to the IgM or IgG responder group (3.6 ± 3.1 vs. 6.3 ± 4.2; p-value = 0.021). The patients with IgM antibody response had a significantly lower CD20+ lymphocytes (11% versus 15% in the groups without IgM antibody response, p-value = 0.031), The percentages of NK cells and CD4+ T cells significantly increased in the patients with IgG antibody response compared to those without IgG antibody response (13% versus 10%, p-value = 0.028, and 41.5% versus 34%; p-value = 0.03, respectively). Moreover, the patients who produced IgM or IgG antibody had significantly higher percentages of total T lymphocytes (64% versus 54%; p-value = 0.017), CD4+ T cells (41% versus 34%; p-value = 0.038), and NK cells (13% versus 9%, p-value = 0.023) compared to the group with no serological response. No significant difference was observed in the percentage of other lymphocyte subsets, including CD8+ T cells, Treg cells, and CD19+ B cells.

Conclusion
Our results suggest that the total T cells, CD4+ T cells, and NK cells percentages are linked to serological response. Moreover, our findings suggested that neutrophil absolute counts and neutrophil-to-lymphocyte ratio may be valuable predictors of IgM or IgG antibody response.
Comparison of saliva with healthcare workers- and patient-collected swabs in the diagnosis of COVID-19 in a large cohort
Authors: Sasikala Mitnala , Sadhana Yelamanchili , Vijayasarathy Ketavarapu , Gupta Anand , Daram Sarala Kumari , Podduturi Naveen Chander Reddy , Reddy Duvvur Nageshwar 
Published: July 2021

Abstract
Background
A considerable amount of evidence demonstrates the potential of saliva in the diagnosis of COVID-19. Our aim was to determine the sensitivity of saliva versus swabs collected by healthcare workers (HCWs) and patients themselves to assess whether saliva detection can be offered as a cost-effective, risk-free method of SARS-CoV-2 detection.

Methods
This study was conducted in a hospital involving outpatients and hospitalized patients. A total of 3018 outpatients were tested. Of these, 200 qRT-PCR-confirmed SARS-CoV-2-positive patients were recruited for further study. In addition, 101 SARS-CoV-2-positive hospitalized patients with symptoms were also enrolled in the study. From outpatients, HCWs collected nasopharyngeal swabs (NPS), saliva were obtained. From inpatients, HCWs collected swabs, patient-collected swabs, and saliva were obtained. qRT-PCR was performed to detect SARS-CoV-2 by TAQPATH assay to determine the sensitivity of saliva detection. Sensitivity, specificity and positive/negative predictive values (PPV, NPV) of detecting SARS-CoV-2 were calculated using MedCalc.

Results
Of 3018 outpatients (asymptomatic: 2683, symptomatic: 335) tested by qRT-PCR, 200 were positive (males: 140, females: 60; aged 37.9 ± 12.8 years; (81 asymptomatic, 119 symptomatic). Of these, saliva was positive in 128 (64%); 39 of 81 asymptomatic (47%),89 of 119 symptomatic patients (74.8%). Sensitivity of detection was 60.9% (55.4–66.3%, CI 95%), with a negative predictive value of 36%(32.9–39.2%, CI 95%).Among 101 hospitalized patients (males:65, females: 36; aged 53.48 ± 15.6 years), with HCW collected NPS as comparator, sensitivity of saliva was 56.1% (47.5–64.5, CI 95%), specificity 63.5%(50.4–75.3, CI95%) with PPV of 77.2% and NPV of 39.6% and that of self-swab was 52.3%(44–60.5%, CI95%), specificity 56.6% (42.3–70.2%, CI95%) with PPV 77.2% and NPV29.7%. Comparison of positivity with the onset of symptoms revealed highest detection in saliva on day 3 after onset of symptoms. Additionally, only saliva was positive in 13 (12.8%) hospitalized patients.

Conclusion
Saliva which is easier to collect than nasopharyngeal swab is a viable alternate to detect SARS-COV-2 in symptomatic patients in the early stage of onset of symptoms. Although saliva is currently not recommended for screening asymptomatic patients, optimization of collection and uniform timing of sampling might improve the sensitivity enabling its use as a screening tool at community level.
Prevalence and correlates of Mycoplasma genitalium infection among patients attending a sexually transmitted infection clinic in Guangdong, China: a cross-sectional study
Authors: Zhang Xiao-Hui , Zhao Pei-Zhen , Ke Wu-Jian , Wang Liu-Yuan , Tso Lai Sze , Chen Zheng-Yu , Liao Yu-Ying , Liang Chun-Mei , Chen Hui-Ru , Ren Xu-Qi , Huang Jin-Mei , Ong Jason J. , Yang Fan , Yang Li-Gang 
Published: July 2021

Abstract
Background
Mycoplasma genitalium (MG) causes urogenital tract infections and is associated with reproductive morbidity. Although MG has been reported across many regions and population groups, it is not yet routinely tested for in China. Our study contributes to current research by reporting the prevalence and correlates of MG infection in patients attending a sexually transmitted infection (STI) clinic in Guangdong from Jan 2017-May 2018.

Methods
Urethral (from 489 men) and endo-cervical (from 189 women) samples, blood samples, and patient histories (via questionnaires) were collected. Doctors clinically diagnosed anogenital warts (GW) during the examination (n = 678). The presence of MG was evaluated using an in-house via polymerase chain reaction protocol. We also tested all participants for herpes simplex virus-2 (HSV-2), Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), syphilis and HIV. Univariate and multivariate logistic regression were used to evaluate factors associated with MG.

Results
MG was detected in 7.2% (49/678) of the patients (men, 7.4%; women, 6.9%). The MG positivity rate was 14.2% among symptomatic patients, and 5.6% for asymptomatic patients, respectively. Only 36.7% (18/49) Mg positive patients were symptomatic. Among the MG-infected patients, 10.2% were co-infected with CT, 6.1% with NG, 8.2% with HSV-2, 4.1% with syphilis and 22.4% with GW. Presentation with clinical symptoms was significantly associated with MG infection [OR = 2.52 (2.03–3.13)]. In our analysis, MG was not associated with other STIs.

Conclusions
MG is a relatively common infection among individuals attending an STI clinic in Guangdong Province. Routine testing of symptomatic patients may be necessary, and more epidemiological studies are needed to provide evidence for future testing guidelines.
Clinicopathological and prognostic study of IgA-dominant postinfectious glomerulonephritis
Authors: Huang Ziyuan , Chen Bo , Zhou Ying , Liang Yan , Qiu Wenxian , Lv Yinqiu , Ding Xiaokai , Zhang Ji , Chen Chaosheng 
Published: July 2021

Abstract
Background
The clinicopathological and prognostic features of IgA-dominant postinfectious glomerulonephritis and its difference from the primary IgA nephropathy remains to be investigated.

Methods
The clinical and pathological data of 6542 patients who underwent renal biopsy from 2009 to 2020 in our hospital were reviewed and 50 patients who met the selection criteria of IgA-dominant postinfectious glomerulonephritis were enrolled to conduct a retrospective and observational single-center study. The selection criteria were: meet the characteristics of IgA dominance or codominance in immunofluorescence, and conform to 3 of the following 5 criteria: 1.Clinical or laboratory evidence show that there is infection before or at the onset of glomerulonephritis; 2.The level of serum complement decreased; 3.Renal pathology is consistent with endocapillary proliferative glomerulonephritis; 4. Glomerular immunofluorescence staining showed complement C3 dominance or codominance; 5. Hump-like subepithelial immune complex deposition was observed under electron microscopy. According to age, sex, renal function (estimated glomerular filtration rate, eGFR) and follow-up time, the control group was constructed with 1:3 matched cases of primary IgA nephropathy. The clinicopathological and prognostic differences between the two groups were analyzed.

Results
The most common histological pattern of IgA-dominant postinfectious glomerulonephritis was acute endocapillary proliferative glomerulonephritis and exudative glomerulonephritis. Immunofluorescence showed mainly IgA deposition or IgA deposition only, mainly deposited in the mesangial area (deposition rate 100 %), with typical C3 high-intensity staining (intensity++~+++), mainly deposited in the mesangial area (deposition rate 92.0 %). The fluorescence intensity of kappa is usually not weaker than lambda. The probability of the appearance of typical hump-like electron deposition under electron microscopy is low. Compared to primary IgA nephropathy, patients with IgA-dominant postinfectious glomerulonephritis had higher proportion of crescents (p = 0. 005) and endocapillary hypercellularity (p < 0.001) in pathological manifestations. Using serum creatinine level doubled of the baseline or reached end-stage renal disease as the endpoint, the prognosis of IgA-dominant postinfectious glomerulonephritis patients was worse than that of primary IgA nephropathy patients (p = 0.013).

Conclusions
The clinicopathological features of patients with IgA-dominant postinfectious glomerulonephritis was different from that of primary IgA nephropathy, and the prognosis was worse.
The association between protease inhibitors and anal cancer outcomes in veterans living with HIV treated with definitive chemoradiation: a retrospective study
Authors: Yoder Alison K. , Lakomy David S. , Dong Yongquan , Raychaudhury Suchismita , Royse Kathryn , Hartman Christine , Richardson Peter , White Donna L. , Kramer Jennifer R. , Lin Lilie L. , Chiao Elizabeth 
Published: July 2021

AbstractBackgroundThe incidence of anal squamous cell carcinoma has been increasing, particularly in people living with HIV (PLWH). There is concern that radiosensitizing drugs, such as protease inhibitors, commonly used in the management of HIV, may increase toxicities in patients undergoing chemoradiation. This study examines treatment outcomes and toxicities in PLWH managed with and without protease inhibitors who are receiving chemoradiation for anal cancer.MethodsPatient demographic, HIV management, and cancer treatment information were extracted from multiple Veterans Affairs databases. Patients were also manually chart reviewed. Among PLWH undergoing chemoradiation for anal carcinoma, therapy outcomes and toxicities were compared between those treated with and without protease inhibitors at time of cancer treatment. Statistical analysis was performed using chi-square, Cox regression analysis, and logistic regression.ResultsA total of 219 PLWH taking anti-retroviral therapy undergoing chemoradiation for anal cancer were identified and included in the final analysis. The use of protease inhibitors was not associated with any survival outcome including colostomy-free survival, progression-free survival, or overall survival (all adjusted hazard ratiop-values> 0.05). Regarding toxicity, protease inhibitor use was not associated with an increased odds of hospitalizations or non-hematologic toxicities; however, protease inhibitor use was associated with increased hospitalizations for hematologic toxicities, including febrile neutropenia (p < 0.01).ConclusionThe use of protease inhibitors during chemoradiation for anal carcinoma was not associated with any clinical outcome or increase in non-hematologic toxicity. Their use was associated with increased hospitalizations for hematologic toxicities. Further prospective research is needed to evaluate the safety and efficacy of protease inhibitors for patients undergoing chemoradiation.
Bronchopulmonary dysplasia in extremely premature infant with congenital lobar emphysema: a case report
Authors: Lin Bingchun , Li Huitao , Yang Chuanzhong 
Published: July 2021

Abstract
Background
Congenital lobar emphysema (CLE) is a congenital pulmonary cystic disease, characterized by overinflation of the pulmonary lobe and compression of the surrounding areas. Most patients with symptoms need an urgent surgical intervention. Caution and alertness for CLE is required in cases of local emphysema on chest X-ray images of extremely premature infants with bronchopulmonary dysplasia (BPD).

Case presentation
Here, we report a case of premature infant with 27 + 4 weeks of gestational age who suddenly presented with severe respiratory distress at 60 days after birth. Chest X-ray and computed tomography (CT) indicated emphysema in the middle lobe of the right lung. The diagnosis of CLE was confirmed by histopathological examinations.

Conclusions
Although extremely premature infants have high-risk factors of bronchopulmonary dysplasia due to their small gestational age, alertness for CLE is necessary if local emphysema is present. Timely pulmonary CT scan and surgical interventions should be performed to avoid the delay of the diagnosis and treatment.
Descriptive epidemiology of measles cases in Bauchi State, 2013–2018
Authors: Ori Polycarp Uchechukwu , Adebowale Ayo , Umeokonkwo Chukwuma David , Osigwe Ugochukwu , Balogun Muhammad Shakir 
Published: July 2021

Abstract
Background
Measles accounts for high morbidity and mortality in children, especially in developing countries. In 2017, about 11,190 measles cases were recorded in Nigeria, including Bauchi State. The aim of this study was to describe the trend and burden of measles in Bauchi State, Nigeria.

Method
We analyzed secondary data of measles cases extracted from the Measles Surveillance data system in Bauchi State from January 2013 to June 2018. The variables extracted included age, sex, doses of vaccination, case location and outcome. Data were analyzed using descriptive statistics, logistic regression, and multiplicative time series model (α = 0.05).

Results
A total of 4935 suspected measles cases with an average annual incidence rate of 15.3 per 100,000 population and 57 deaths (Case Fatality Rate, CFR: 1.15%) were reported. Among the reported cases, 294 (6%;) were laboratory-confirmed, while clinically compatible and epi-linked cases were 402 (8%) and 3879 (70%), respectively. Of the 4935 measles cases, 2576 (52%) were males, 440 (9%) were under 1 year of age, and 3289 (67%) were between 1 and 4 years. The average annual incidence rate among the 1–4 year age-group was 70.3 per 100,000 population. The incidence rate was lowest in 2018 with 2.1 per 100,000 and highest in 2015 with 26.2 per 100,000 population. The measles cases variation index per quarter was highest in quarter 1 (198.86), followed by quarter 2 (62.21) and least in quarter 4 (10.37) of every year. Only 889 (18%) of the measles cases received at least one dose of measles vaccine, 2701 (54.7%) had no history of measles vaccination while 1346 (27.3%) had unknown vaccination status. The fatality of measles in Bauchi State were significantly associated with being under 5 years (AOR = 5.58; 95%CI: 2.19–14.22) and not having at least a dose of MCV (OR = 7.14; 95%CI: 3.70–14.29).

Conclusion
Measles burden remains high in Bauchi State despite a decrease in its incidence over the study years. Most of the cases occurred in the first quarter of every year. Improved routine measles surveillance for prompt case management could reduce the burden of the disease in Bauchi State.
Income in relation to obesity measures in an East German adult population: findings from the LIFE-Adult-Study
Authors: Enzenbach Cornelia , Kowall Bernd 
Published: July 2021

Abstract
Background
Obesity has been postulated to be a consequence of economic disadvantage. However, epidemiological studies failed to demonstrate a consistent link between income and body fat indicators. We examined income as a possible cause of obesity in an East German general population, focusing on appropriate representation of study variables, as well as on confounding and modification of the income-obesity association.

Methods
We used data of 9599 participants in the baseline examination of the LIFE-Adult-Study, conducted in the city of Leipzig from 2011 to 2014. Body mass index (BMI) and waist circumference (WC) as obesity measures were based on standardised measurements, net equivalised income (NEI) on self-reports. We estimated adjusted means of BMI and WC within NEI categories representing the range from risk of poverty to affluence. We stratified the analyses by gender, age, and education.

Results
A substantial part of the age-adjusted associations of income with obesity measures was attributable to other SES indicators. Adjusted for these variables, NEI was comparably associated with BMI and WC. Among women, BMI and WC decreased across NEI categories. The inverse associations tended to be stronger at non-working age (≥ 65 years) than at working age (< 65 years). Conversely, among working-age men, BMI and WC increased with increasing NEI. Among older men, risk of poverty was related to higher values of the obesity measures. The aforementioned associations were predominantly stronger in highly educated participants compared to those with medium/low education. The differences in mean BMI and WC between persons at risk of poverty and higher income groups were rather small, ranging from 1 to 2 kg/m2 for BMI and 2 to 4 cm for WC.

Conclusions
Our investigation indicates an association between income and body fatness in an East German adult population that depends on the sociodemographic context of the people. However, it does not suggest that income disparities are a major driver of body fat accumulation in this population. Differential selection of study participants, error in the measurement of long-term income, and possibly reverse causality may have affected our conclusions.