Miracle-dz/UniFAR-FTUs huggingface dataset:
Users' Guides to the Medical Literature: IX. A Method for Grading Health Care Recommendations

THE ULTIMATE PURPOSE of applied health research is to improve health care. Summarizing the literature to adduce recommendations for clinical practice is an important part of the process. Recently, the health sciences community has reduced the bias and imprecision of traditional literature summaries and their associated recommendations through the development of rigorous criteria for both literature overviews 1-3 and practice guidelines. 4,5 Even when recommendations come from such rigorous approaches, however, it is important to differentiate between those based on weak vs strong evidence. Recommendations based on inadequate evidence often require reversal when sufficient data become available, 6 while timely implementation of recommendations based on strong evidence can save lives. 6 In this article, we suggest an approach to classifying strength of recommendations. We direct our discussion primarily at clinicians who make treatment recommendations that they hope their colleagues will follow. However, we believe that any clinician who attends to
An image processing method for investigating the morphology of cereal endosperm cells

ABSTRACT In cereal seeds, the number, morphology and development of endosperm cells are closely related to grain quality, weight and yield. Endosperm cells differ morphologically in different regions of the seed. Nevertheless, it is important to be able to analyze the morphology of cereal endosperm cells. We established an image processing method to enhance the outlines of endosperm cells. The endosperm cell wall was traced precisely using the “pen tool” in Photoshop software (PS). The tracing was defined as the “work path” and was highlighted using the PS “brush tool. ” Images of mature rice, maize and wheat endosperm sections stained with different methods were analyzed using this method. Combined with the whole sections of mature and developing cereal kernels, the processed image exhibited clearly the morphology of endosperm cells in any region of endosperm and at any stage of endosperm development. The processed image was more accurate and efficient for analyzing morphological characteristics than the unprocessed image.
The analgesic efficacy of paravertebral block for percutaneous nephrolithotomy

Abstract Introduction: The analgesic efficacy of paravertebral block for percutaneous nephrolithotomy remains controversial. We conduct a systematic review and meta-analysis to explore the analgesic efficacy of paravertebral block for patients with percutaneous nephrolithotomy. Methods: We have searched PubMed, EMbase, Web of science, EBSCO, and Cochrane library databases, and randomized controlled trials (RCTs) assessing analgesic efficacy of paravertebral block for percutaneous nephrolithotomy are included in this meta-analysis. Results: Five RCTs are included in the meta-analysis. Overall, compared with control group after percutaneous nephrolithotomy, paravertebral block is associated with the decrease in analgesic consumption (standard mean difference (Std. MD) = −1.55; 95% confidence interval (CI) = −2.18 to −0.92; P < . 00001) and additional analgesics (risk ratio (RR) = 0.17; 95% CI = 0.07 to 0.44; P = . 0003), prolonged time to first analgesic requirement (Std. MD = 1.51; 95% CI = 0.26 to 2.76; P = .02). There is no statistical difference of adverse events including nausea or vomiting (RR = 0.51; 95% CI = 0.11 to 2.35; P = .38), or itching (RR = 0.69; 95% CI = 0.26 to 1.81; P = .45) between 2 groups. Conclusions: Paravertebral block is effective for pain control after percutaneous nephrolithotomy.
Purification and Characterization of Pathogenesis Related Class 10 Panallergens

Oral allergy syndrome (OAS) describes an allergic reaction where an individual sensitized by pollen allergens develops symptoms after eating certain foods. OAS is caused by cross-reactivity among a class of proteins ubiquitous in plants called pathogenesis related class 10 (PR-10) proteins. The best characterized PR-10 protein is Bet v 1 from birch pollen and its putative function is binding hydrophobic ligands. We cloned a subset of seven recombinant PR-10 proteins from pollens, peanuts, and hazelnuts and developed a standard purification method for them. Immunoglobulin E (IgE) binding of purified PR-10 proteins was analyzed by ImmunoCAP ISAC microarray and enzyme-linked immunosorbent assays (ELISAs) with sera from allergic patients. We investigated the binding activities of PR10s by testing 16 different ligands with each protein and compared their secondary structures using circular dichroism (CD). The PR-10s in this study had very similar CD spectra, but bound IgE with very different affinities. All seven proteins showed a similar pattern of binding to the polyphenol ligands (resveratrol, flavonoids, and isoflavones) and variable binding to other potential ligands (fatty acids, sterols, and plant hormones). We suggest our protocol has the potential to be a near-universal method for PR-10 purification that will facilitate further research into this important class of panallergens.
Intranasal delivery of human umbilical cord Wharton's jelly mesenchymal stromal cells restores lung alveolarization and vascularization in experimental bronchopulmonary dysplasia

Bronchopulmonary dysplasia (BPD) is a devastating lung condition that develops in premature newborns exposed to prolonged mechanical ventilation and supplemental oxygen. Significant morbidity and mortality are associated with this costly disease and effective therapies are limited. Mesenchymal stem/stromal cells (MSCs) are multipotent cells that can repair injured tissue by secreting paracrine factors known to restore the function and integrity of injured lung epithelium and endothelium. Most preclinical studies showing therapeutic efficacy of MSCs for BPD are administered either intratracheally or intravenously. The purpose of this study was to examine the feasibility and effectiveness of human cord tissue‐derived MSC administration given via the intranasal route. Human umbilical cord tissue MSCs were isolated, characterized, and given intranasally (500 000 cells per 20 μL) to a hyperoxia‐induced rat model of BPD. Lung alveolarization, vascularization, and pulmonary vascular remodeling were restored in animals receiving MSC treatment. Gene and protein analysis suggest the beneficial effects of MSCs were attributed, in part, to a concerted effort targeting angiogenesis, immunomodulation, wound healing, and cell survival. These findings are clinically significant, as neonates who develop BPD have altered alveolar development, decreased pulmonary vascularization and chronic inflammation, all resulting in impaired tissue healing. Our study is the first to report the intranasal delivery of umbilical cord Wharton's jelly MSCs in experimental BPD is feasible, noninvasive, and an effective route that may bear clinical applicability.
Using Social Support Matter in the Association of Post-Traumatic Cognitions and Perceived Social Support? Comparison of Female Survivors of Intimate Partner Violence With and Without a History of Child Abuse

The association between high levels of post-traumatic stress disorder (PTSD) symptoms and low levels of perceived social support is well-documented in the trauma literature; research on processes that may underlie this association is less common. The current study examined negative attitudes about using social support as a potential link between negative post-traumatic cognitions about the world and self, one aspect of PTSD, and perceived social support in two groups of female survivors of intimate partner violence: those who had a history of child abuse (n = 153; IPV/CA+) and those who did not (n = 96; IPV/CA−). Negative attitudes about using social support were found to be an important link between negative post-traumatic cognitions and social support for both groups. IPV survivors with a history of child abuse had higher levels of negative post-traumatic cognitions about the world (d = .32) and self (d = .33), greater negative attitudes about using social support (d = .35), and lower perceived social support from family (d = .48), compared with IPV survivors without a history of child abuse. These results support the relevance of negative attitudes about using social support as one important factor in the relationship between PTSD symptoms and social support in interpersonal trauma survivors and highlight the impact that negative attitudes about using social support can have on the trauma survivor’s functioning.
PKR-dependent cytosolic cGAS foci are necessary for intracellular DNA sensing

Intracellular DNA provokes cytoplasmic cGAS condensation, which requires the helicase G3BP1 and the RNA-dependent kinase PKR. Stronger together Aberrant intracellular recognition of self-DNA is controlled by the spatial restriction of the DNA sensor cGAS. To define the interactions that may control cGAS subcellular localization, Hu et al. used mass spectrometry and immunoprecipitation to confirm that endogenous cGAS bound to the nucleotide helicase G3BP1, which is involved in stress granule formation. After DNA stimulation of human cells, cGAS associated in an RNA-dependent manner with G3BP1 and was found in cytoplasmic foci that also contained mRNA and the RNA-dependent kinase PKR. Formation of cytoplasmic cGAS condensates necessary for DNA-stimulated type I interferon production required G3BP1 and PKR activity. Together, these data suggest that G3BP1 cytoplasmic foci act as hubs that may coordinate DNA and RNA nucleic acid sensing. Cyclic GMP-AMP synthase (cGAS) is a major sensor of cytosolic DNA from invading pathogens and damaged cellular organelles. Activation of cGAS promotes liquid-like phase separation and formation of membraneless cytoplasmic structures. Here, we found that cGAS bound G3BP1, a double-stranded nucleic acid helicase involved in the formation of stress granules. Loss of G3BP1 blocked subcellular cGAS condensation and suppressed the interferon response to intracellular DNA and DNA virus particles in cells. Furthermore, an RNA-dependent association with PKR promoted G3BP1 foci formation and cGAS-dependent interferon responses. Together, these results indicate that PKR promotes the formation of G3BP1-dependent, membraneless cytoplasmic structures necessary for the DNA-sensing function of cGAS in human cells. These data suggest that there is a previously unappreciated link between nucleic acid sensing pathways, which requires the formation of specialized subcellular structures.
Addition of Endothelin A-Receptor Blockade Spoils the Beneficial Effect of Combined Renin-Angiotensin and Soluble Epoxide Hydrolase Inhibition: Studies on the Course of Chronic Kidney Disease in 5/6 Nephrectomized Ren-2 Transgenic Hypertensive Rats

Introduction: Previous studies in Ren-2 transgenic hypertensive rats (TGR) after 5/6 renal ablation (5/6 NX) have shown that besides pharmacological blockade of the renin-angiotensin system (RAS) also increasing kidney tissue epoxyeicosatrienoic acids (EET) levels by blocking soluble epoxide hydrolase (sEH), an enzyme responsible for degradation of EETs, and endothelin type A (ETA) receptor blockade retards chronic kidney disease (CKD) progression. This prompted us to evaluate if this progression will be alleviated by the addition of sEH inhibitor and ETA receptor antagonist to the standard complex blockade of RAS (angiotensin-converting enzyme inhibitor plus angiotensin II type 1 receptor blocker) in rats with established CKD. Methods: The treatment regimens were initiated 6 weeks after 5/6 NX in TGR, and the follow-up period was 60 weeks. Results: The addition of sEH inhibition to RAS blockade improved survival rate, further reduced albuminuria and renal glomerular and kidney tubulointerstitial injury, and attenuated the decline in creatinine clearance – all this as compared with 5/6 NX TGR treated with RAS blockade alone. Addition of ETA receptor antagonist to the combined RAS and sEH blockade not only offered no additional renoprotection but, surprisingly, also abolished the beneficial effects of adding sEH inhibitor to the RAS blockade. Conclusion: These data indicate that pharmacological strategies that combine the blockade of RAS and sEH could be a novel tool to combat the progression of CKD. Any attempts to further extend this therapeutic regimen should be made with extreme caution.
Heat Treatment at an Early Age Has Effects on the Resistance to Chronic Heat Stress on Broilers

Simple Summary In this study, we investigated early heat exposure to a chronic heat-stressed group, of which has effects on growth performance, liver-specific enzymes (GOT; glutamic oxalacetic transaminase, and GPT; glutamic pyruvate transaminase), neuro (dopamine and serotonin) and stress (corticosterone) hormones, and the expression of HSPs (heat shock proteins), HSFs (heat shock factors), and pro-inflammatory cytokines. Chronic heat stress and early heat exposed groups reduced body weight, feed intake, and GOT, GPT, serotonin in the serum, and the protein expression of HSPs in liver tissue. At the same time, HSP70, HSP27, TNF-α, IFNG, and IL-6 gene expression were up-regulated in the early heat exposed group. According to study results regarding the broilers, early heat exposure has no effects on growth performance, physiology, and HSP protein expressions. Abstract This study was conducted to investigate the effects of early heat conditioning on growth performance, liver-specific enzymes (GOT and GPT), neuro-hormones (dopamine and serotonin), stress hormones (corticosterone), and the expression of HSPs (heat shock proteins), HSFs (heat shock factors), and pro-inflammatory cytokines under chronic high temperature. Broilers were raised with commercial feed and supplied with water ad libitum under conventional temperature. We separated the broilers into three groups: the control without any heat exposure (C), chronic heat-stressed group (CH), and early and chronic heat-stressed group (HH). At 5 days of age, the HH group was exposed to high temperatures (40 °C for 24 h), while the remaining groups were raised at a standard temperature. Between days 6 and 20, all three groups were kept under optimal temperature. From 21 to 35 days, the two heat-stressed groups (CH and HH) were exposed to 35 °C. Groups exposed to high temperature (CH and HH) showed significantly lower body weight and feed intake compared to the control. GOT and GPT were lower expressed in the CH and HH groups than the control group. In addition, the protein expressions of HSPs were down-regulated by chronic heat stress (CH and HH groups). The gene expressions of HSP60 and HSF3 were significantly down-regulated in the CH and HH groups, while HSP70 and HSP27 genes were up-regulated only in the HH group compared with the control group. The expression of pro-inflammatory cytokine genes was significantly up-regulated in the HH group compared with the control and CH groups. Thus, exposure of early Heat stress (HS) to broilers may affect the inflammatory response; however, early heat exposure did not have a positive effect on chronic HS of liver enzymes and heat shock protein expression.
Extradural Contralateral C7 Nerve Root Transfer in a Cervical Posterior Approach for Treating Spastic Limb Paralysis: A Cadaver Feasibility Study.

STUDY DESIGN Anatomic study in nine fresh-frozen cadavers. OBJECTIVE To confirm the anatomical feasibility of transferring the extradural ventral roots (VRs) and dorsal roots (DRs) of contralateral C7 nerves to those of the ipsilateral C7 nerves respectively through a cervical posterior approach. SUMMARY OF BACKGROUND DATA The contralateral C7 nerve root transfer technique makes breakthrough for treating spastic limb paralysis. However, its limitations include large surgical trauma and limited indications. METHODS Nine fresh-frozen cadavers (four females and five males) were placed prone, and the feasibility of exposing the bilateral extradural C7 nerve roots, separation of the extradural C7 VR and DR, and transfer of the VR and DR of the contralateral C7 to those of the ipsilateral C7 on the dural mater were assessed. The pertinent distances and the myelography results of each specimen were analyzed. The acetylcholinesterase (AChE) and antineurofilament 200 (NF200) double immunofluorescent staining were preformed to determine the nerve fiber properties. RESULTS A cervical posterior midline approach was made and the laminectomy was performed to expose the bilateral extradural C7 nerve roots. After the extradural C7 VR and DR are separated, the VR and DR of the contralateral C7 have sufficient lengths to be transferred to those of the ipsilateral C7 on the dural mater. The myelography results showed that the spinal cord is not compressed after the nerve anastomosis. The AChE and NF200 double immunofluorescent staining showed the distal ends of the contralateral C7 VRs were mostly motor nerve fibers, and the distal ends of the contralateral C7 DRs were mostly sensory nerve fibers. CONCLUSIONS Extradural contralateral C7 nerve root transfer in a cervical posterior approach for treating spastic limb paralysis is anatomically feasibleLevel of Evidence: 5.
Optimized Extraction of Insect Genomic DNA for Long-Read Sequencing

Long-read sequencing technologies continue to increase the length of reads, and at present can average read lengths of >20 kb up to 60–80 kb. Now the challenge is to extract genomic DNA of sufficient fragment size and quality to support longer read lengths. We developed a successful method to consistently obtain high-quality long genomic DNA from insects. The optimal developmental stage of insects for genomic DNA extraction was determined to be the pupal stage, eliminating DNA from ingested food and reducing contamination by chitinous material that can interfere with extraction. Improved results were obtained by a modified procedure of a commercial genomic DNA extraction kit. Initially, soft pupal tissue of the red flour beetle, Tribolium castaneum, was disrupted in the kit lysis buffer using Teflon micropestles. Modifications to the kit protocol also included gentle mixing by inversion of the tube, instead of harsh vortexing steps, and using wide-bore pipette tips in transferring fractions containing genomic DNA. Data from one sample were provided as an example of successful downstream library production and sequencing. While the technique has been optimized for insects, extractions from tissues of other organisms using these modified procedures also may improve long-read sequencing results.
Selection for tandem stop codons in ciliate species with reassigned stop codons

The failure of mRNA translation machinery to recognize a stop codon as a termination signal and subsequent translation of the 3’ untranslated region (UTR) is referred to as stop codon readthrough, the frequency of which is related to the length, composition, and structure of mRNA sequences downstream of end-of-gene stop codons. Secondary in-frame stop codons within a few positions downstream of the primary stop codons, so-called tandem stop codons (TSCs), serve as backup termination signals, which limit the effects of readthrough: polypeptide product degradation, mislocalization, and aggregation. In this study, ciliate species with UAA and UAG stop codons reassigned to code for glutamine are found to possess statistical excesses of TSCs at the beginning of their 3’ UTRs. The overrepresentation of TSCs in these species is greater than that observed in standard code organisms. Though the overall numbers of TSCs are lower in most species with alternative stop codons because they use fewer than three unique stop codons, the relatively great overrepresentation of TSCs in alternative-code ciliate species suggests that there exist stronger selective pressures to maintain TSCs in these organisms compared to standard code organisms.
Multifractal Analysis of Histopathological Tissue Images

Histopathological classification and grading of biopsy specimens play an important role in early cancer detection and prognosis. Nottingham scoring system is one of the standard grading procedures used in breast cancer assessment, where three parameters, Mitotic Count (MC), Nuclear Pleomorphism (NP), and Tubule Formation (TF) are used for prognostic information. The grading takes into account the deviations in cellular structures and appearance from normal, using measures such as density, size, colour and regularity. Cell structures in tissue images are also known to exhibit multifractal characteristics. This paper looks at the multifractal properties of several graded biopsy specimens and analyses the dependency and variation of the fractal parameters with respect to the scores assigned by pathologists. Keywords-Breast cancer assessment; Multifractal spectra; Image analysis; Histopathological classification; Feature detection; Cancer grading
Introducing new point-of-care tests for common infections in publicly funded clinics in South Africa: a qualitative study with primary care clinicians

Broad-spectrum antibiotics are routinely prescribed empirically in the resource-poor settings for suspected acute common infections, which drive antimicrobial resistance. Point-of-care testing (POCT) might increase the appropriateness of decisions about whether and which antibiotic to prescribe, but implementation will be most effective if clinician’s perspectives are taken into account. Objectives To explore the perceptions of South African primary care clinicians working in publicly funded clinics about: making antibiotic prescribing decisions for two common infection syndromes (acute cough, urinary tract infection); their experiences of existing POCTs; their perceptions of the barriers and opportunities for introducing (hypothetical) new POCTs. Design, method, participants, setting Qualitative semistructured interviews with 23 primary care clinicians (nurses and doctors) at publicly funded clinics in the Western Cape Metro district, South Africa. Data were analysed using thematic analysis. Results Clinicians reported that their antibiotic prescribing decisions were influenced by their clinical assessment, patient comorbidities, social factors (eg, access to care) and perceived patient expectations. Their experiences with currently available POCTs were largely positive, and they were optimistic about the potential for new POCTs to: support evidence-based prescribing decisions that might reduce unnecessary antibiotic prescriptions; reduce the need for further investigations; support effective communication with patients, especially when antibiotics were unlikely to be of benefit. Resources and workflow disruption were seen as the main barriers to uptake into routine care. Conclusions Clinicians working in publicly funded clinics in the Western Cape Metro of South Africa saw POCTs as potentially useful for positively addressing both clinical and social drivers of the overprescribing of broad-spectrum antibiotics, but were concerned about the resource implications and disruption of existing patient workflows.