Miracle-dz/UniFAR-FTUs huggingface dataset:
Field Assessment of Gravel Loss on Unsealed Roads in Australia

The gravel loss is a major limitation for unsealed roads and it needs major maintenance annually. The continual process of gravel loss leads to the unsustainability of these roads. The unsealed road management faces several issues, viz., difficulty to forecast behavior, huge data collection needs, and a vulnerability in the service and maintenance practices. The quality of gravel material also plays a major role in the process of gravel loss. In view of the aforementioned, appropriate revisions to ARRB material specifications are proposed in this study. The gravel material as per modified ARRB specifications is used on the unsealed road network in the Scenic Rim Regional Council in the state of Queensland. Gravel loss monitoring stations were established over the entire region in order to assess the gravel loss and the implication of using a better quality of gravel material. This study discusses the gravel loss monitoring approaches, data analyses, and improved material specification for gravel. It is found that the modified gravel used on unsealed road performs better than conventionally used gravel.
Influenza A Virus Pre-Infection Exacerbates Pseudomonas aeruginosa-Mediated Lung Damage Through Increased MMP-9 Expression, Decreased Elafin Production and Tissue Resilience

Individuals with impaired immune responses, such as ventilated and cystic fibrosis patients are often infected with Pseudomonas aeruginosa (P.a) bacteria, and a co-infection with the Influenza virus (IAV) is often present. It has been known for many years that infection with IAV predisposes the host to secondary bacterial infections (such as Streptococcus pneumoniae or Staphylococcus aureus), and there is an abundance of mechanistic studies, including those studying the role of desensitization of TLR signaling, type I IFN- mediated impairment of neutrophil chemokines and antimicrobial production, attenuation of IL1β production etc., showing this. However, little is known about the mechanistic events underlying the potential deleterious synergy between Influenza and P.a co-infections. We demonstrate here in vitro in epithelial cells and in vivo in three independent models (two involving mice given IAV +/– P.a, and one involving mice given IAV +/– IL-1β) that IAV promotes secondary P.a-mediated lung disease or augmented IL-1β-mediated inflammation. We show that IAV-P.a-mediated deleterious responses includes increased matrix metalloprotease (MMP) activity, and MMP-9 in particular, and that the use of the MMP inhibitor improves lung resilience. Furthermore, we show that IAV post-transcriptionally inhibits the antimicrobial/anti-protease molecule elafin/trappin-2, which we have shown previously to be anti-inflammatory and to protect the host against maladaptive neutrophilic inflammation in P.a infections. Our work highlights the capacity of IAV to promote further P.a-mediated lung damage, not necessarily through its interference with host resistance to the bacterium, but by down-regulating tissue resilience to lung inflammation instead. Our study therefore suggests that restoring tissue resilience in clinical settings where IAV/P.a co-exists could prove a fruitful strategy.
PELP1 Suppression Inhibits Gastric Cancer Through Downregulation of c-Src-PI3K-ERK Pathway

Background: Proline-, glutamic acid-, and leucine-rich protein 1 (PELP1), a co-activator of estrogen receptors alpha, was confirmed to be directly associated with the oncogenic process of multiple cancers, especially hormone-dependent cancers. The purpose of our research was to explore the biological function, clinical significance, and therapeutic targeted value of PELP1 in gastric cancer (GC). Methods: The expression status of PELP1 in GC cell lines or tissues was analyzed through bioinformatics data mining. Thirty-six GC tissue chip was applied to demonstrate the results of bioinformatics data mining assayed by immunohistochemical method. The expression status of PELP1 in GC cell lines was also analyzed using western blot. Correlation analysis between PELP1 expression and clinicopathological parameter was performed. Kaplan-Meier survival analysis was applied to analyze the relationship between PELP1 expression and total survival time. Three pairs of siRNA were designed to silence the expression of PELP1 in GC. After PELP1 was silenced by siRNA or activated by saRNA, the growth, plate colony formation, migration and invasion ability of the GC cell or normal gastric epithelium cell line was tested in vitro. Cell cycle was tested by flow cytometry. Nude mice xenograft experiment was performed after PELP1 was silenced. The downstream molecular pathway regulated by PELP1 was explored. Molecular docking tool was applied to combine chlorpromazine with PELP1. The inhibitory effect of chlorpromazine in GC was assayed, then it was tested whether PELP1 was a therapeutic target of chlorpromazine in GC. Results: PELP1 expression was elevated in GC cell lines and clinical GC tissue samples. PELP1 silence by siRNA compromised the malignant traits of GC. PELP1 expression positively correlated with tumor invasion depth, lymph node metastasis, tissue grade, TNM stage, but had no correlation with patient age, sex, tumor size, and tumor numbers. Kaplan-Meier survival analysis revealed high PELP1 expression had a shorter survival period in GC patients after follow-up. Q-PCR and western blot revealed PELP1 suppression in GC decreased expression of the c-Src-PI3K-ERK pathway. It was also implied that chlorpromazine (CPZ) can inhibit the malignant traits of GC and downregulate the expression of PELP1. Conclusions: In a word, PELP1 is an oncogene in gastric cancer and c-Src-PI3K-ERK pathway activation may be responsible for its tumorigenesis, PELP1 may be a potential therapeutic target of chlorpromazine in GC.
Coexistence of Two blaNDM–5 Genes Carried on IncX3 and IncFII Plasmids in an Escherichia coli Isolate Revealed by Illumina and Nanopore Sequencing

The emergence of carbapenem-resistant Enterobacteriaceae poses a significant threat to public health worldwide. Here, we reported a multidrug-resistant Escherichia coli strain with two different blaNDM–5-carrying plasmids from China. Illumina short-read and MinION long-read whole genome sequencing were performed. Genomic analysis found that one blaNDM–5 gene together with mphA was located on a 55-kb IncX3 plasmid, while the other blaNDM–5 gene was on a novel 68-kb IncFII plasmid. Susceptibility testing and quantitative reverse transcription PCR results further indicated that the transconjugants with the IncX3 plasmid exhibited higher-level carbapenem resistance and expression of blaNDM–5 than those with both plasmids or the IncFII plasmid. Two other β-lactamase genes (blaCTX–M–15 and blaOXA–1) were also detected on another 160-kb IncF plasmid. This is the first report of coexistence of two blaNDM–5-carrying plasmids in a single bacterial isolate, highlighting the genetic complexity of NDM-5 carbapenemase circulation, and the urgent need for continued active surveillance.
Lack of Rule-Adherence During Mountain Gorilla Tourism Encounters in Bwindi Impenetrable National Park, Uganda, Places Gorillas at Risk From Human Disease

Mountain gorillas (Gorilla beringei beringei) are an endangered primate species, with ~43% of the 1,063 individuals that remain on the planet today residing in Bwindi Impenetrable National Park (BINP) in southwestern Uganda. These primates are at the heart of a growing tourism industry that has incentivized their continued protection, but close proximity between humans and gorillas during such encounters presents well-documented risks for disease transmission. The Uganda Wildlife Authority (UWA) has developed rules to help protect the health of the gorillas, limiting each habituated gorilla group to a single 60 min visit each day by a group of no more than 8 tourists, and emphasizing that humans maintain a >7 m distance from gorillas at all times. A number of studies have documented that not all tour groups respect these rules. This project assesses rule-adherence during gorilla tourism encounters at BINP using both observational and survey-based data collected during the tourism high season between May and August, 2014. Observational data from 53 treks reveal that groups of 1–11 tourists engaged in gorilla viewing encounters between 46 and 98 min in duration. Although 96% of pre-trek briefings conducted by park rangers emphasized the need to maintain >7 m human-gorilla spacing, the 7 m distance rule was violated in over 98% (52 out of 53) of the tours examined in this study. Observational data were collected at 2 min intervals during gorilla-viewing encounters, documenting the nearest distance between any tourist and a gorilla (n = 1,604), of which 1,094 observations (68.2%) took place at a distance less than or equal to 7 m. Importantly, the 7 m rule was violated in visits to all of the gorilla groups habituated during the time of the study. In 224 observations (~14%, per 1,604 total), human-gorilla spacing was 3 m or less. Survey data (n = 243) revealed promising opportunities to improve tourist understanding of and adherence to park rules, with 73.6% of respondents indicating that they would be willing to utilize a precautionary measure of wearing a face-mask during encounters to protect gorilla health.
Large Underestimation of Intraspecific Trait Variation and Its Improvements

Intraspecific trait variation (ITV) is common feature of natural communities and has gained increasing attention due to its significant ecological effects on community dynamics and ecosystem functioning. However, the estimation of ITV per se has yet to receive much attention, despite the need for accurate ITV estimation for trait-based ecological inferences. It remains unclear if, and to what extent, current estimations of ITV are biased. The most common method used to quantify ITV is the coefficient of variation (CV), which is dimensionless and can therefore be compared across traits, species, and studies. Here, we asked which CV estimator and data normalization method are optimal for quantifying ITV, and further identified the minimum sample size required for ±5% accuracy assuming a completely random sample scheme. To these ends, we compared the performance of four existing CV estimators, together with new simple composite estimators, across different data normalizations, and sample sizes using both a simulated and empirical trait datasets from local to regional scales. Our results consistently showed that the most commonly used ITV estimator (CV 1= σsample /μsample ), often underestimated ITV—in some cases by nearly 50%—and that underestimation varies largely among traits and species. The extent of this bias depends on the sample size, skewness and kurtosis of the trait value distribution. The bias in ITV can be substantially reduced by using log-transforming trait data and alternative CV estimators that take into consideration the above dependencies. We find that the CV4 estimator, also known as Bao's CV estimator, combined with log data normalization, exhibits the lowest bias and can reach ±5% accuracy with sample sizes greater than 20 for almost all examined traits and species. These results demonstrated that many previous ITV measurements may be substantially underestimated and, further, that these underestimations are not equal among species and traits even using the same sample size. These problems can be largely solved by log-transforming trait data first and then using the Bao's CV to quantify ITV. Together, our findings facilitate a more accurate understanding of ITV in community structures and dynamics, and may also benefit studies in other research areas that depend on accurate estimation of CV.
Prognosis for different patterns of distant metastases in patients with uterine cervical cancer: a population-based analysis

Background: Uterine cervical cancer (UCC) is a common malignant tumor in women. We conducted this work to provide a though description on the patterns of distant metastases and to investigate the relevant factors for prognosis of UCC patients based on a large population. Patients and methods: UCC patients with FIGO stage IVB, being the study group, were identified from the Surveillance, Epidemiology, and End Result (SEER) database from 2010 to 2016. UCC patients with same inclusion criteria, being validation group, were identified from Tianjin First Central Hospital from 2004 to 2017. Patterns of distant metastases were described according to the number of metastatic sites. Survival of different patterns were calculated and prognostic factors were investigated by Cox hazard regression analysis. Results: Distant metastases were recorded in 1448 UCC patients among whom 295 patients (30.8%) developed metastases in two or more organs. Compared with the median OS of 8 (95%CI, 7.07-8.93) months in the patients with the single site, worse survival of 5 (95%CI, 4.29-5.71) months was noticed in the patients with multiple metastases. Age ≥ 65 years, black race, higher grade, higher T stage and more metastatic sites were proved to be the prognostic factors for all the patients in the advanced stage and the results were partly validated in the validation cohort. Moreover, black race and higher T-stage for the patients with the single metastatic sites and age ≥ 65, uninsured status, surgical treatment and metastatic pattern for the patients with two metastatic sites were prognostic factors. No independent factor was found in patients with three or more metastases. Conclusion: Around 70% of the patients suffered one site distant metastasis in UCC patients with IVB stage while 30% with multiple metastases and a significantly reduced survival. Different survivals and prognostic factors were noticed for different patterns of distant metastases.
Prevalence and Antibiotic Resistance Pattern of Salmonella Isolated from Caecal Contents of Exotic Chicken in Debre Zeit and Modjo, Ethiopia

A cross-sectional study was conducted between December, 2013, and May, 2014, to determine the prevalence and antibiotic resistance feature of Salmonella isolated from broilers slaughtered in Debre Zeit and Modjo towns, Ethiopia. A total of 384 caecal content samples were collected for microbiological examination following the standard techniques and procedures outlined by the International Organization for Standardization to isolate Salmonella. The sensitivity of the isolates subjected to nine antimicrobials was tested by the Kirby–Bauer disk diffusion method. The overall prevalence of Salmonella was 14.6%, and its occurrence differ significantly by farm (p < 0.05). The occurrence of the bacteria was not statistically different in the midland (15.2%) and lowland (13.3%) (p > 0.05) and between males (13.5%) and females (15.6) (p > 0.05). Of the 50 isolates, 48 were resistant to at least one drug. Multidrug resistance was recorded in 43 (86.0%) of the isolates. The study demonstrated considerable prevalence and high antimicrobial resistant Salmonella in exotic chicken and indicates the potential importance of chickens as source of foodborne salmonellosis and multiple antimicrobial resistance of Salmonella. Improving the hygienic practice of farms could help to reduce the occurrence of Salmonella in farms. Further studies are needed to describe the risk factors associated with the emergence of drug-resistant Salmonella in chicken.
Prevalence and Associated Factors of Tuberculosis among Adult Household Contacts of Smear Positive Pulmonary Tuberculosis Patients Treated in Public Health Facilities of Haramaya District, Oromia Region, Eastern Ethiopia

Background Tuberculosis is an infectious airborne disease caused by Mycobacterium tuberculosis. It still remains a major public health problem which affects all age groups. Risk of exposure is higher in household contact than members of the general population. Objective The aim of this study was to assess the prevalence and associated factors of tuberculosis among adult household contacts of smear positive pulmonary tuberculosis in Haramaya district, Oromia Region, Eastern Ethiopia from February to March, 2019. Method A community based cross-sectional study design was conducted. A total of 454 study participants were selected using systematic sampling method from all adult household contacts of smear positive pulmonary tuberculosis patients treated from July 2017 to December 2018. Data were collected using a pretested and structured questionnaire; and laboratory examination was processed using fluorescent smear microscope. Logistic regression analysis was used to identify the factors associated with the infection of pulmonary tuberculosis and a statistically significant association was declared at P-value < 0.05. Result The overall prevalence of pulmonary tuberculosis among adult household contacts was 7.8% (95% CI: 5.8–10.0). The risk factors for tuberculosis infection among household contacts were eating meals less than three times per day (AOR = 4.31; 95% CI: 1.61, 11.55), drinking raw milk (AOR = 4.12; 95% CI: 1.43, 11.90), having family history of tuberculosis with more than one index case (AOR = 2.7; 95% CI: 1.02, 6.92), living in poor ventilated houses (AOR = 4.02; 95% CI: 1.38, 11.76), and living in inadequate size of living room (AOR = 3.4; 95% CI: 1.30, 8.86). Conclusion In this study, the prevalence of tuberculosis among adult household contacts of smear positive pulmonary tuberculosis is high. Eating meals less than three times per day, drinking raw milk, living in poor ventilated houses, and inadequate sizes of the rooms were identified as contributing factors. Therefore, we recommend that the transmission of tuberculosis can potentially be reduced by a better contact tracing and treatment strategies along with appropriate health education.
Sustained Intraocular Pressure Rise after the Treat and Extend Regimen at 3 Years: Aflibercept versus Ranibizumab

Purpose To determine the risk factors associated with sustained intraocular pressure (IOP) rise in patients enrolled in the treat and extend (T&E) protocol receiving aflibercept/ranibizumab therapy for 3 years. Design Retrospective, observational chart review. Setting. Multicentric. Patients. 789 patients (1021 eyes; 602 males) enrolled in T&E using aflibercept/ranibizumab for diabetic macular edema (DME), wet age-related macular degeneration (AMD), or macular edema in retinal vein occlusion (RVO). Intervention. The history, examination (clinical and special investigations), and treatment records were thoroughly scrutinized. Sustained IOP rise was defined as a rise in IOP above baseline by ≥6 mmHg and/or >24 mmHg on 2 or more consecutive visits. The Wilk–Shapiro test was used for confirming normality of data. The Mantel–Haenszel test and generalized estimating equations were used to analyse multicentric data as well as to analyse data from both eyes of the same patients in the event that both eyes were under therapy. The relative risk, chi-square test (with and without Yates' correction), and univariate and multivariate analysis were used wherever appropriate. Statistical significance was set at P < 0.05. The primary outcome measure was the determination of risk factors for sustained IOP rise with ranibizumab/aflibercept therapy. Secondary outcome measures included determining the incidence of IOP rise (short term and sustained), visual field, and retinal nerve fibre layer (RNFL) changes. Results The mean follow-up was 42.4 months. Male gender, South Asian ethnicity, older age, presence of AMD and vein occlusion, use of ranibizumab, higher number of injections, narrow angles, switch to bevacizumab/ranibizumab, and preexisting glaucoma were associated with sustained IOP rise. No significant visual field and RNFL changes were seen. The overall incidence was 8.91%. No patient required filtering surgery. No patient with IOP rise returned to baseline. Conclusion IOP rise is an important consideration as the chronicity of the condition can eventually lead to glaucomatous changes in eyes with already compromised vision. Follow-ups and use of appropriate therapy can be determined correspondingly.
Adverse Outcomes and Economic Burden of Congenital Adrenal Hyperplasia Late Diagnosis in the Newborn Screening Absence

Abstract Objective To establish short- and long-term adverse outcome frequencies related to a late diagnosis of congenital adrenal hyperplasia (CAH) in the absence of newborn screening (NBS) and to determine respective treatment costs, which have never been reported. Design A retrospective analysis of a CAH cohort diagnosed without NBS. Methods We evaluated medical record data concerning 195 patients (141 females) diagnosed with CAH through clinical suspicion and confirmed using hormonal and CYP21A2 analysis, who were followed from 1980 to 2016 at Sao Paulo University. We measured mortality, dehydration, mental impairment frequencies, and hospitalization length outcomes in the salt-wasting form; the frequency of genetic females raised as males in both forms, frequency of depot GnRh analog (GnRha) and GH therapies in the simple virilizing form, and related outcome costs were calculated. Results Mortality rates and associated costs, varying from 10% to 26% and from $2,239,744.76 to $10,271,591.25, respectively, were calculated using the Brazilian yearly live-births rate, estimated productive life years, and gross domestic product. In the salt-wasting form, 76% of patients were hospitalized, 8.6% were mentally impaired, and 3% of females were raised as males (total cost, $86,230/salt-wasting patient). GnRha and growth hormone were used for 28% and 14% of simple virilizing patients, respectively, and 18% of females were raised as males (preventable cost, $4232.74/simple virilizing patient). Conclusions A late CAH diagnosis leads to high mortality and morbidity rates, notably increasing public health costs, and may result in physical and psychological damage that is not easily measurable.
Comparison of risk factors between colon cancer and rectum cancer in a single medical center hospital, Taiwan

Introduction Colorectal cancer (CRC) is rapidly increasing in developed countries. In Taiwan, the incidence rate of CRC has increased during the past decade, but the 5-year survival has remained at approximately 63%. In this study, we sought to determine the 5-year survival rate of patients diagnosed with colon and rectum cancer and to determine factors affecting survival. Material and methods All patients from the Taiwan Cancer Database of the medical center hospital in North Taiwan between 2007 and 2013 were identified. Survival analysis was performed using Kaplan-Meier curves, and differences between the curves were analyzed using the log-rank test. Cox proportional hazards regression models were used to analyze survival by each variable. Results A total of 869 patients were included: 554 (63.8%) patients had colon cancer and 315 (36.2%) had rectum cancer. The mean survival time was 71.27 ±1.27 months (colon group: 71.90 ±1.58 months; rectum group: 67.88 ±1.95 months). There was no significant difference (p = 0.493) between patients who had colon or rectum cancer. The forward stepwise Cox regression analysis results indicated that perineural invasion, distant metastasis, age, pathological differentiation grade, and obstruction were statistically significant for patients who had CRC, colon cancer or rectum cancer. Conclusions The long-term survival from CRC, colon cancer and rectum cancer remains promising, as 68.66%, 69.11% and 67.90% of patients are alive 5 years after being diagnosed, respectively. Perineural invasion was found to be an important factor related to the survival of patients who have CRC. Thus, early detection of CRC may help improve survival.