Miracle-dz/UniFAR-FTUs huggingface dataset:
Increasing resistance to bacterial leaf streak in rice by editing the promoter of susceptibility gene OsSULRT3; 6

Rice (Oryza sativa L.) is an important cereal crop consumed by almost half the world population and is vital for global food security. Bacterial leaf streak (BLS), which is caused by Xanthomonas oryzae pv. oryzicola (Xoc), is a devastating rice disease in Asia, Africa and Australia (Nino-Liu et al., 2006; Ji et al., 2014). Like other Xanthomonads, Xoc utilizes the type III secretion system (T3SS) to translocate effector proteins directly into host cells to suppress plant immunity (Nino-Liu et al., 2006; Yuan et al., 2021).
Foot and Ankle Problems in Patients With Rheumatoid Arthritis in 2019: Still an Important Issue

To study the prevalence of foot pain in patients with rheumatoid arthritis (RA) and whether including a 12‐joint foot count in addition to the 28‐joint count (from the Disease Activity Score 28 [DAS28]) improved detection of foot or ankle pain. In addition, the association between the self‐reported foot and ankle score (SEFAS), patient‐reported function, and disease‐specific factors was studied.
Travel time to emergency care not by geographic time, but by optimal time: A nationwide cross-sectional study for establishing optimal hospital access time to emergency medical care in South Korea

Increase in travel time, beyond a critical point, to emergency care may lead to a residential disparity in the outcome of patients with acute conditions. However, few studies have evaluated the evidence of travel time benchmarks in view of the association between travel time and outcome. Thus, this study aimed to establish the optimal hospital access time (OHAT) for emergency care in South Korea. We used nationwide healthcare claims data collected by the National Health Insurance System database of South Korea. Claims data of 445,548 patients who had visited emergency centers between January 1, 2006 and December 31, 2014 were analyzed. Travel time, by vehicle from the residence of the patient, to the emergency center was calculated. Thirteen emergency care–sensitive conditions (ECSCs) were selected by a multidisciplinary expert panel. The 30-day mortality after discharge was set as the outcome measure of emergency care. A change-point analysis was performed to identify the threshold where the mortality of ECSCs changed significantly. The differences in risk-adjusted mortality between patients living outside of OHAT and those living inside OHAT were evaluated. Five ECSCs showed a significant threshold where the mortality changed according to their OHAT. These were intracranial injury, acute myocardial infarction, other acute ischemic heart disease, fracture of the femur, and sepsis. The calculated OHAT were 71–80 min, 31–40 min, 70–80 min, 41–50 min, and 61–70 min, respectively. Those who lived outside the OHAT had higher risks of death, even after adjustment (adjusted OR: 1.04–7.21; 95% CI: 1.03–26.34). In conclusion, the OHAT for emergency care with no significant increase in mortality is in the 31–80 min range. Optimal travel time to hospital should be established by optimal time for outcomes, and not by geographic time, to resolve the disparities in geographical accessibility to emergency care.
The effects of centralizing cancer surgery on postoperative mortality: A systematic review and meta-analysis

Objectives To review the evidence of the effects of centralization of cancer surgery on postoperative mortality. Methods We searched Medline, Embase, Cinahl, Cochrane and Scopus (up to November 2019) for studies that (i) assessed the effects of centralization of cancer surgery policies on in-hospital or 30-day mortality, or (ii) described changes in both postoperative mortality for a surgical intervention and degree of centralization using reduction in the number of hospitals or increases in the proportion of patients undergoing cancer surgery at high volume hospitals as proxy. PRISMA guidelines were followed. We estimated pooled odds ratios (OR) and conducted meta-regression to assess the relationship between degree of centralization and mortality. Results A total of 41 studies met our inclusion criteria of which 15 evaluated the effect of centralization policies on postoperative mortality after cancer surgery and 26 described concurrent changes in the degree of centralization and postoperative mortality. Policy evaluation studies mainly used before-after designs (n = 13) or interrupted time series analysis (n = 2), mainly focusing on pancreatic, oesophageal and gastric cancer. All but one showed some degree of reduction in postoperative mortality, with statistically significant effects demonstrated by six studies. The pooled odds ratio for centralization policy effect was 0.68 (95% Confidence interval: 0.54–0.85; I2 = 80%). Meta-regression analysis of the 26 descriptive studies found that an increase of the proportion of patients treated at high volume hospitals was associated with greater reduction in postoperative mortality. Conclusions Centralization of cancer surgery is associated with reduced postoperative mortality. However, existing evidence tends to be of low quality and estimates of the effect size are likely inflated. There is a need for prospective studies using more robust approaches, and for centralization efforts to be accompanied by well-designed evaluations of their effectiveness.
Reversible switching of primary cells between normal and malignant state by oncogenic virus KSHV and CRISPR/Cas9‐mediated targeting of a major viral latent protein

Viral infection has been implicated in the pathogenesis of a plethora of human diseases. Although antiviral therapies effectively confront the viral spread and infection, how to completely eradicate the viral genome from infected cells remains a challenge. In this study, we demonstrated the reversible switching of primary cells between normal and malignant states by an oncogenic virus Kaposi's sarcoma‐associated herpesvirus (KSHV) and CRISPR/Cas9‐mediated targeting of a major viral latent protein. Primary cells can be transformed into malignant status by infection of KSHV, while elimination of the KSHV genome from latent KSHV‐infected cells reverses KSHV‐transformed primary cells back to a “normal state” by CRISPR/Cas‐mediated knockout of viral major latent gene LANA. As a proof of concept, we demonstrated efficient elimination of KSHV episome in KSHV‐associated primary effusion lymphoma cells resulting in the induction of apoptosis by liposome‐encapsulated CRISPR/Cas9 ribonucleoprotein complexes (Lipo/Cas9‐LANAsgRNA). Our work illustrates CRISPR/Cas as a promising technology for eliminating oncogenic viruses from persistently infected cells by taking advantage of the genetic differences between viral and cellular genomes. Compared to traditional antiviral therapy, our study offer an approach for antagonizing human oncogenic virus‐related cancers by directly targeting as well as clearing viral genomes.
Phenotypic plasticity is not a cline: thermal physiology of an intertidal barnacle over 20 degrees of latitude.

Our understanding of the plastic and evolutionary potential of ectothermic organisms and their populational impacts in the face of rapid global change remains limited. Studies attempting on the relationship between the magnitude of thermal variability across latitude and the degree of phenotypic plasticity exhibited by marine ectotherms are inconclusive. We state that the latter arises from the narrow range of thermal variability captured by the limited span of the latitudinal gradients studied to date. Using a mechanistic ecophysiological approach and a satellite-based assessment of the relevant environmental variables (i.e. temperature and food availability), we studied individuals of the intertidal barnacle Jehlius cirratus from seven local populations widely spread along the Humboldt current System that spanning two biogeographic regions. At the same time, we synthesized published information on the local abundance of our study species across a total of 76 sites representing 20 degrees of latitude, and spanning from 18 to 42°S. We examined the effects of latitude and environmental variability on metabolic rate plasticity, thermal tolerance (thermal breadth and thermal safety margins) and their impacts on the abundance of this widespread marine invertebrate. We demonstrate that the phenotypic plasticity of metabolic rate in J. cirratus populations is not related to latitude. In turn, thermal breadth is explained by the temperature variability each population experiences. Furthermore, we found clinal variation with a poleward decrease of the critical thermal minimum, suggesting that episodic extreme low temperatures represent a ubiquitous selective force on the lower thermal limit for ectotherms. Across our study gradient, plasticity patterns indicate that populations at the equatorial extreme are more vulnerable to a warming climate, while populations located in the biogeographic transitional zone (i.e. high environmental heterogeneity), on the center of the gradient, display higher levels of phenotypic plasticity, and may represent a genetic buffer for the effects of ocean warming. Together, our results suggest the existence of a fitness trade-off involving the metabolic cost of plasticity and population density that is evident only across the vast latitudinal gradient examined.
Exploring the Experiences of Families of Latino Children Newly Diagnosed With Autism Spectrum Disorder

ABSTRACT: Objective: Understanding families' experiences from their initial developmental concerns through the first several months after autism spectrum disorder (ASD) diagnosis might help explain persistent disparities in age of diagnosis for low-income Latino children and those whose parents speak a primary language other than English. We explored these experiences among Latino parents of children recently diagnosed with ASD to develop a richer understanding of this critical juncture. Method: We conducted semistructured interviews with Latino parents of children diagnosed with ASD in the previous 3 months who were receiving follow-up care through a large, hospital-based outpatient practice. Interviews were recorded, transcribed verbatim, translated, and analyzed using an iterative process. Results: Twenty parents participated in a semistructured interview approximately 3 months after their child was diagnosed with ASD. All respondents were female and Latina, 90% spoke Spanish, and 95% of children received Medicaid. We identified the following 3 themes from their experiences: (1) When parents first shared their concerns about their child's development with professionals, they felt unheard. (2) Parents were surprised that the diagnostic process for ASD relied on parental description of child development and behavior and observation of the child, not on medical tests. (3) Receiving an ASD diagnosis was a life-altering event for parents, and how that diagnosis was communicated by clinicians had a significant impact on families. Conclusion: Parents of young Latino children identified several barriers throughout the process of ASD identification and diagnosis that have important implications for improving clinician communication with families.
Costs, Evidence, Context and Values: Journalists’ and Policy Experts’ Recommendations for U.S. Health Policy Coverage

ABSTRACT Health policy plays a critical role in determining a state’s or nation’s overall population health, and health system change has been a priority for a majority of Americans for at least a decade. News coverage can influence health policy development, but little research has examined the quality of that coverage, in part because no consensus exists regarding what information health policy stories should include. This paper describes a series of in-depth interviews with eight health policy experts and 12 experienced journalists who have covered health policy. While rejecting the notion of strict quality criteria that could be applied to all health policy stories, the interviewees agreed on several factors that would improve health policy coverage. They recommended that health policy stories should include information about financial costs to consumers, evidence that a policy will have its intended effect, historical context for the policy, and “relatable hooks” that help consumers understand which groups a policy will affect and how. In addition, the interviewees stressed the importance of building policy coverage on trustworthy sources representing multiple viewpoints and the need to recognize how audience members’ values influence their acceptance and interpretation of evidence. These findings provide an important foundation for future research examining the impact of health policy reporting on both public opinion and public policy development.
The pan‐genome of the cultivated soybean (PanSoy) reveals an extraordinarily conserved gene content

Summary Studies on structural variation in plants have revealed the inadequacy of a single reference genome for an entire species and suggest that it is necessary to build a species‐representative genome called a pan‐genome to better capture the extent of both structural and nucleotide variation. Here, we present a pan‐genome of cultivated soybean (Glycine max), termed PanSoy, constructed using the de novo genome assembly of 204 phylogenetically and geographically representative improved accessions selected from the larger GmHapMap collection. PanSoy uncovers 108 Mb (˜11%) of novel nonreference sequences encompassing 3621 protein‐coding genes (including 1659 novel genes) absent from the soybean ‘Williams 82’ reference genome. Nonetheless, the core genome represents an exceptionally large proportion of the genome, with >90.6% of genes being shared by >99% of the accessions. A majority of PAVs encompassing genes could be confirmed with long‐read sequencing on a subset of accessions. The PanSoy is a major step towards capturing the extent of genetic variation in cultivated soybean and provides a resource for soybean genomics research and breeding.
Optimasi Pengambilan Antosianin dari Kulit Buah Naga Merah (Hylocereus polyrhizus) Sebagai Pewarna Alami pada Makanan

The addition of synthetic colors in foods in an attempt to attract the attention of consumers, not a ban, but if the dye used is a dye that is unusual for the food, it is harmful to health. One source of natural pigments that can be used is the red dragon fruit skin. These skins contain anthocyanins potential as a dye. In this reasearch, the observed red dragon fruit skin moisture content and size of the powder. It also conducted a stirring speed variation during the extraction process. While variable temperature, time, and solvent refers to the optimum conditions of research that has been done. Analysis of the results was conducted to determine pH, anthocyanin concentration and yield results. Based on the results obtained, the smaller the water content contained in the skin, giving absorbance values are higher. This shows that extractable anthocyanins levels are also higher. The lowest levels of the skin can be achieved in this study was 6%. The smaller the grain size, the higher the anthocyanin content. The smallest grain size achieved was 100 mesh. The highest mixing speed in this study was 300 rpm, the higher the stirring speed, the higher the anthocyanin content fetched. Organoleptic tests were conducted to study the effect of anthocyanins on the quality of the food shows that the addition of anthocyanins provide the appropriate color and do not significantly affect flavor and aroma. So it can be used as a natural dye for food.
Structural variations on Salmonella biofilm by exposition to river water

ABSTRACT Biofilm formation, as adapting strategies, is the result of stressful conditions that Salmonella faces in hostile environments like surface water. We evaluated river water effect on Salmonella biofilm formation ability in terms of physical, morphological characteristics and chemical composition. A new morphotype SPAM (soft, pink and mucoid) was detected in Oranienburg strains S-76 and S-347 (environmental and clinical isolate). Oranienburg serotypes showed very marked behavior in adherence, pellicle liquid-air and resistance, being Oranienburg S-76 the strongest biofilm producer. All strains when exposed to river water presented an overlapping mucoid layer in the morphotype and increased their motility except Oranienburg S-347. The most motile was Typhimurium (control) and the least Infantis S-304 (clinical isolate). Mannose, glucose, galactose and ribose were the main biofilm sugar components; type and concentration of sugar suggest a morphotype/serotype dependent pattern. Strong morphotypes expressed in this study may be an effective protective strategy for Salmonella in hostile environments.
Podocentric view of glomerular proteinuria: Focused on cytoskeletal changes and toward promising targeted therapies and challenges

Among renal cells, podocytes (glomerular epithelial cells) are the most critical to prevent plasma proteins from excessive loss by forming their sophisticated foot processes (FP) and slit diaphragms (SD). A general finding in the glomeruli of patients with nephrotic syndrome is the foot processes “effacement” resulted from dysregulated actin cytoskeleton reorganization. Ultrastructural analysis in patients with nephrotic syndrome has demonstrated that such changes tend to be dynamic and can sometimes be reversible. In a more molecular sense, injured podocytes can no longer maintain their tight regulation and “retract” their FP, but not “efface” them. Past studies have revealed multiple exquisite mechanisms and arrays of proteins participating in the regulation of cytoskeletal rearrangement, and these mechanisms serve as potential targets to treat. A major challenge to develop specific therapies is the targeted mechanism has to be crucial and specific enough for podocyte‐oriented kidney diseases, and it would be even better to manifest in most of the glomerulonephritis. Studies have shown many approaches targeting different mechanisms, but none of them has been proved to be effective in clinical medicine. Up to the present, Abatacept (Orencia) is the first (and the only) clinical targeted therapy demonstrating limited success. It inhibits the co‐stimulatory response of B7‐1 (CD80) induced in various types of glomerulonephritis. Future clinical studies have to be expanded to substantiate this highly specific targeted therapy because the Abatacept effect is not generally accepted even within the nephrology community. Nevertheless, there are ongoing searches for specific treatment targeting podocytes through various approaches.
The virtual loss function in the summary perception of motion and its limited adjustability

Humans can grasp the “average” feature of a visual ensemble quickly and effortlessly. However, it is largely unknown what is the exact form of the summary statistic humans perceive and it is even less known whether this form can be changed by feedback. Here we borrow the concept of loss function to characterize how the summary perception is related to the distribution of feature values in the ensemble, assuming that the summary statistic minimizes a virtual expected loss associated with its deviation from individual feature values. In two experiments, we investigated a random-dot motion estimation task to infer the virtual loss function implicit in ensemble perception and see whether it can be changed by feedback. On each trial, participants reported the average moving direction of an ensemble of moving dots whose distribution of moving directions was skewed. In Experiment 1, where no feedback was available, participants’ estimates fell between the mean and the mode of the distribution and were closer to the mean. In particular, the deviation from the mean and toward the mode increased almost linearly with the mode-to-mean distance. The pattern was best modeled by an inverse Gaussian loss function, which punishes large errors less heavily than the quadratic loss function does. In Experiment 2, we tested whether this virtual loss function can be altered by feedback. Two groups of participants either received the mode or the mean as the correct answer. After extensive training up to five days, both groups’ estimates moved slightly towards the mode. That is, feedback had no specific influence on participants’ virtual loss function. To conclude, the virtual loss function in the summary perception of motion is close to inverse Gaussian, and it can hardly be changed by feedback.
Associations Between Blood Trace Element Levels and Nutritional Status in Maintenance Hemodialysis.

OBJECTIVE(S) We aimed to investigate the associations between blood trace element levels and nutritional status in patients undergoing maintenance hemodialysis (MHD). METHODS This cross-sectional study included patients undergoing MHD who were treated at our center in September 2019. Clinical and demographic data and blood samples were collected before hemodialysis sessions, and the levels of manganese, lead, selenium, zinc, and copper were measured by inductively coupled plasma mass spectrometry. The Simplified Nutritional Appetite Questionnaire scale was used to assess patient appetite. Skinfold thickness, bicep circumference, upper arm muscle circumference, 7-point Subjective Global Assessment, Nutritional Risk Screening 2002 (NRS 2002), and Geriatric Nutritional Risk Index (GNRI) were used to assess patient nutritional status. Univariate and multivariate logistic regression analyses were performed to study the relationship between trace elements and nutritional indicators. RESULTS In total, 118 patients (64 males and 54 females) were included, with a median dialysis vintage of 34.0 months (16.0-54.5 months) and an average age of 63.20 ± 14.26 years. Malnourished patients, as defined by the GNRI, Subjective Global Assessment, and NRS 2002, accounted for 28.0%, 49.2%, and 26.3% of enrolled patients, respectively. The multivariate binary logistic regression showed that higher blood copper levels were independently associated with nutritional risk defined as GNRI ≤91.2 (odds ratio [OR] = 1.003, 95% confidence interval [CI] = 1.000-1.006; P = .020), whereas lower blood zinc levels (OR = 0.634, 95% CI = 0.439-0.916; P = .015), blood zinc < 4.220 mg/L (OR = 3.723, 95% CI = 1.274-10.879; P = .016), lower blood selenium levels (OR = 0.959, 95% CI = 0.929-0.990; P = .010), and blood selenium < 85 μg/L (OR = 5.568, 95% CI = 1.039-29.840; P = .045) were independently associated with a nutritional risk defined as NRS 2002 ≥ 3. CONCLUSION(S) Higher levels of blood copper and lower levels of blood zinc and selenium were independently associated with higher nutritional risk in MHD patients.
Mycobacterial IclR family transcriptional factor Rv2989 is specifically involved in isoniazid tolerance by regulating the expression of catalase encoding gene katG

Transcriptional factors are essential for bacteria to adapt diverse environmental stresses, especially upon exposure to antibiotics. Mycobacterium tuberculosis, the causative agent of tuberculosis which inflicts around one third of the global population, contains three IclR family transcriptional factors, namely Rv1719, Rv1773c and Rv2989. In this study, MSMEG_2386, the homolog of Rv2989 in Mycobacterium smegmatis, was deleted by homologous recombination and complemented. The gene did not affect the growth in conventional culture. However, the growth of deletion mutants upon isoniazid (INH) exposure was severely delayed. This growth defect is specific to INH and not observed in other antibiotics tested, including rifampicin, capreomycin, norfloxacin and ethionamide. The transcription of katG and enzymatic activity of its encoding product catalase were elevated in the MSMEG_2386 deleted M. smegmatis mutants. The survival of MSMEG_2386 deletion mutant within U937 macrophages was markedly reduced compared with the wild type strain. These results improve our understanding of the role of IclR family transcriptional factors in INH resistance in mycobacteria.