Miracle-dz/UniFAR-FTUs huggingface dataset:
Traditional Mutagenesis Meets Functional Genomics

Most of the genes of an organism are known from sequence, but most of the phenotypes are obscure. Thus, reverse genetics has become an important goal for many biologists. However, reverse-genetic methodologies are not similarly applicable to all organisms. In the general strategy for reverse genetics that we call TILLING (for Targeting Induced Local Lesions in Genomes), traditional chemical mutagenesis is followed by high-throughput screening for point mutations. TILLING promises to be generally applicable. Furthermore, because TILLING does not involve transgenic modifications, it is attractive not only for functional genomics but also for agricultural applications. Here, we present an overview of the status of TILLING methodology, including Ecotilling, which entails detection of natural variation. We describe public TILLING efforts in Arabidopsis and other organisms, including maize (Zea mays) and zebrafish. We conclude that TILLING, a technology developed in plants, is rapidly being adopted in other systems.
Development of a functional in vitro assay as a novel tool for the standardization of allergen extracts in the human system

Background: Biochemical and immunochemical methods used for batch control of allergen extracts rely on the binding of IgE molecules to allergens. They do not measure the ability of a protein to induce type I allergic reactions. Therefore, a biological assay was established that is based on the cellular mechanisms of allergies in order to assess the cross‐linking capacity of allergens.
A randomized trial of a representational intervention for cancer pain: does targeting the dyad make a difference?

OBJECTIVE To determine the efficacy in overcoming attitudinal barriers to reporting cancer pain and using analgesics of an educational intervention presented to patients accompanied by a significant other (SO) as compared with patients alone. DESIGN Patient-SO pairs (N = 161) were randomized to the dyad condition (patient and SO received the intervention), solo condition (patient received the intervention), or care as usual. Dyad and solo conditions received the intervention at baseline (T1) and 2 and 4 weeks later. MAIN OUTCOME MEASURES Patients' and SOs' attitudes about analgesic use and patients' pain outcomes (pain severity, pain relief, interference with life, negative mood, and global quality of life [QOL]) at T1, 5 weeks later (T2), and 9 weeks later (T3). RESULTS Completers' analyses revealed no significant differences between groups at T2. At T3, patients in the dyad and the solo groups showed greater decreases in attitudinal barriers as compared with controls. T1-T3 changes in patients' barriers mediated between the dyad and solo interventions and pain severity, pain relief, pain interference, negative mood, and global QOL. CONCLUSION The intervention was no more efficacious when it was presented to dyads than to patients alone. Conditions under which SOs should be included in interventions need to be determined.
Apolipoprotein A5, a Crucial Determinant of Plasma Triglyceride Levels, Is Highly Responsive to Peroxisome Proliferator-activated Receptor α Activators*

The recently discovered APOA5 gene has been shown in humans and mice to be important in determining plasma triglyceride levels, a major cardiovascular disease risk factor. apoAV represents the first described apolipoprotein where overexpression lowers triglyceride levels. Since fibrates represent a commonly used therapy for lowering plasma triglycerides in humans, we investigated their ability to modulate APOA5 gene expression and consequently influence plasma triglyceride levels. Human primary hepatocytes treated with Wy 14,643 or fenofibrate displayed a strong induction of APOA5 mRNA. Deletion and mutagenesis analyses of the proximal APOA5 promoter firmly demonstrate the presence of a functional peroxisome proliferator-activated receptor response element. These findings demonstrate that APOA5 is a highly responsive peroxisome proliferator-activated receptor α target gene and support its role as a major mediator for how fibrates reduce plasma triglycerides in humans.
Serum fasting lipid profile in children and adolescents with β-thalassaemia major in southern Pakistan.

OBJECTIVE Serum fasting lipid profile has been studied in various clinical spectrum of Beta (β)-thalassaemia syndrome. Premature cardiac impairment in thalassaemia major appears primarily due to iron accumulation and oxidative injury; however it might be a sequel of abnormal lipoprotein concentrations. The rational of this study is to analyse the serum fasting lipid profile in cardiovascular disease free β-thalassaemia major (β-TM) patients. Relationships with age, gender, haematological parameters, liver enzymes and serum ferritin were observed. METHOD Fasting serum lipid levels, liver function test (LFT), complete blood count (CBC) and serum ferritin were measured in 36 patients with homozygous β-TM from March 2012 to March 2014. Patients were stratified into two groups, age≤15 and >15 years, to determine the possible lipid profile distinction in relation to age. RESULTS 17 were males and 19 were females, with median age of 12.0 years. The mean total cholesterol (TC) and triglyceride (TG) were 5.01±1.32 and 8.36±5.28 mmol/L respectively. High TG was detected in 36.1%, while high density lipoprotein cholesterol (HDL) and low density lipoprotein cholesterol (LDL) were markedly low, 0.98±0.51 and 2.35±1.22 mmol/L respectively. No statistically significant difference was noted between the two age groups. The median TC to HDL ratio (TC:HDL) was elevated, 5.7 (4.0). We established significant correlation of total bilirubin with TC (r=-0.4), HDL (r=-0.5) and LDL (r=-0.4) (P<0.05). CONCLUSION Dyslipidaemia in β-TM patients is irrespective of age and gender including low HDL and high TC:HDL, whilst high TC:HDL may contribute as a significant risk marker for future cardiac events in these patients.
Endothelial Function in Patients with Proteinuric Primary Glomerulonephritis

Background: Cardiovascular disease is the commonest cause of mortality among patients with end-stage renal disease. Endothelial function and inflammation have previously been shown to be abnormal among such individuals, and are known to be important factors in the progression of atherosclerosis. The aim of this study was to assess endothelial function early in the natural history of renal disease. Methods: Patients with primary glomerulonephritis, and healthy controls were recruited. In addition to routine laboratory assessment of renal function and proteinuria, assays were undertaken to measure CRP, vWF, VCAM and ICAM. Furthermore, a direct assessment of microvascular endothelial function was undertaken, using laser Doppler imaging to measure perfusion to areas of skin under the influence of transdermally delivered vasodilator agents. Results: Data were collected from 39 patients and 22 controls. No patient was taking anti-platelet agents, statins or angiotensin-converting enzyme inhibitors at the time of endothelial function assessment. All 3 biomarkers of endothelial function were significantly elevated in the patient group compared to controls: ICAM 455 versus 359 ng/ml (p = 0.009), VCAM 1,101 versus 771 ng/ml (p = 0.007) and vWF 184 versus 125 IU/ml (p < 0.001). These differences remained significant after adjusting for blood pressure and body mass index. Endothelium-dependent and endothelium-independent vascular responses were blunted in the patient group, compared to controls (AUC: 2,204 vs. 3,721 PU for dependent and 2,190 vs. 3,555 PU for independent responses). Conclusions: Microvascular endothelial and vascular smooth muscle function is abnormal in patients with primary glomerulonephritis and moderate proteinuria but well-maintained renal function. We believe these findings to be of particular importance as they compare 2 well-matched groups in the absence of the confounding influence of drugs known to affect endothelial function.
Prospective multicentre cohort study of patient‐reported outcomes after cholecystectomy for uncomplicated symptomatic cholecystolithiasis

Up to 33 per cent of patients with uncomplicated symptomatic cholecystolithiasis report persistent pain after cholecystectomy. The aim of this study was to determine characteristics associated with patient‐reported absence of abdominal pain after cholecystectomy, improved abdominal symptoms, and patient‐reported positive cholecystectomy results in a prospective cohort multicentre study.
Dipropyl 4,8-dioxo-1H,5H-2,6-dioxa-3a,4a,7a,8a-tetraazacyclopenta[def]fluorene-8b,8c-dicarboxylate

The title compound, C16H22N4O8, is a glycoluril derivative with two propoxycarbonyl substituents on the convex face of the glycoluril system. The dihedral angle between the five-membered rings in the glycoluril unit is 72.70 (2)°. The oxadiazinane six-membered ring displays a normal chair conformation. One of the propyl groups is disordered over two positions with site occupancies of 0.557 (7) and 0.443 (7). Intermolecular C—H⋯O hydrogen bonds are effective in the stabilization of the crystal structure.
Antifibroblast antibodies from systemic sclerosis patients are internalized by fibroblasts via a caveolin-linked pathway.

OBJECTIVE Fibroblast activation is a crucial event in the development of systemic sclerosis (SSc). Antifibroblast autoantibodies (AFAs), detectable in the sera of SSc patients, are able to induce a proinflammatory phenotype on cultured fibroblasts. This study was undertaken to investigate the mechanisms of the interaction between AFAs and living fibroblasts. METHODS We coupled to fluorescein 1) IgG purified from AFA-positive and AFA-negative SSc sera (as assessed by cellular enzyme-linked immunosorbent assay) and 2) single healthy donor and pooled normal IgG. The interaction of IgG with living cultured fibroblasts from healthy individuals and from a patient with SSc was visualized by real-time confocal microscopy. Intracellular colocalization of caveolin and internalized AFA-positive IgG was assessed by immunofluorescence. RESULTS AFA-positive IgG bound to living fibroblasts and was internalized with a cytoplasmic fibrillar pattern, in contrast to AFA-negative IgG. In the IgG tested, no correlation with antinuclear antibody activity was found. Preincubation of fibroblasts with normal IgG did not affect internalization. Internalized AFA-positive IgG colocalized with caveolin, and internalization was entirely inhibited by disassembling fibroblast caveolae with filipin. CONCLUSION The finding that both normal and pathologic fibroblasts specifically internalized AFA-positive, but not AFA-negative, IgG demonstrates that AFAs in SSc patient sera interact with constitutively expressed membrane molecules on fibroblasts, via an Fc-independent mechanism. The results of colocalization and inhibition experiments suggest that microdomains containing caveolin are involved in the interaction between AFAs and fibroblasts. These data, together with the reported ability of AFAs to activate fibroblasts, provide evidence for a role of AFAs in the pathogenesis of SSc.
Behaviour of multipotent maxillary bone-derived cells on beta-tricalcium phosphate and highly porous bovine bone mineral.

OBJECTIVES The aim of this study was to test the applicability of multipotent maxillary cells (MMC) for cell therapy concepts and to evaluate their in vitro behaviour on two different bone substitutes. MATERIAL AND METHODS Cells isolated from maxillary bone from 10 donors were expanded using media containing human platelet lysate (HPL) replacing foetal bovine serum and differentiated towards both the osteogenic and the adipogenic lineage. Surface markers were determined by fluorescence-activated cell sorting analysis. Calcium deposits, alkaline phosphatase (ALP) and osteocalcin (OC) were used as biomarkers of osteogenic differentiation. Oil Red O was used to verify adipogenic differentiation. The osteogenic lineage and undifferentiated controls were further cultured on natural bone mineral of bovine origin (BioOss) and beta-tricalcium phosphate (Vitoss) scaffolds. Scaffold efficacy and cell migration were evaluated with live cell imaging. RESULTS Isolated cells presented characteristics of bone marrow (BM)-stromal cells and could easily be expanded to clinical scales. Cells expressed osteogenic and adipogenic markers when cultured with inductive media. There were no obvious differences in cell migration and growth behaviour between the two bone substitutes, but significantly higher OC expression was observed on BioOss scaffolds. Both osteogenically differentiated and undifferentiated cell lines expressed ALP activity on the scaffolds. CONCLUSION Isolated maxillary cells demonstrate multipotent in vitro characteristics comparable with those of BM-stromal cells. HPL can predictably be used for clinical-scale expansion of MMCs. Both grafting materials provide potential carrier characteristics when loaded with MMCs.
Predicting the medical school progress of minority students who participated in a preparatory program

&NA; The grade‐point averages (GPAs), Medical College Admission Test (MCAT) scores, and Student Progress Committee (SPC) ratings of 75 minority students who had attended a preparatory program at Southern Illinois University School of Medicine at some period from 1976 through 1986 were analyzed to determine how these variables related to the retention and progress of these students in medical school. Although those retained had higher SPC ratings than those not retained, stepwise regression revealed that none of the variables predicted retention. The MCAT Reading score, however, was significantly higher for students who progressed on schedule; it was the only significant predictor of progress.
Risk factors for uterine rupture among women who attempt a vaginal birth after a previous cesarean: a case-control study.

OBJECTIVE To identify risk factors associated with uterine rupture among term pregnancies attempting a vaginal birth after a previous cesarean. STUDY DESIGN A case-control study was done of 348 uterine ruptures in Massachusetts between 1991 and 1998, initially screened by ICD-9 code and confirmed by medical record review, with 424 control women with a trial of labor randomly selected proportional to cases on year of delivery. Multivariable regression was used to estimate odds ratios and 95% confidence intervals. RESULTS Successful previous vaginal birth decreased risk for uterine rupture, and gestation > 40 weeks and macrosomia increased risk. Oxytocin for induction increased risk, with a slightly lower effect when used for augmentation. Prostaglandin use in conjunction with oxytocin did not have an additive uterine rupture risk. Women using epidural analgesia have an increased uterine rupture risk. CONCLUSION Certain labor management practices increase the risk for uterine rupture 2-3 times, although the absolute increase is small from a baseline uterine rupture rate of 0.5% to 1.0-1.5%. The association between epidural analgesia and uterine rupture deserves further study.
Gastric juvenile polyposis associated with germline SMAD4 mutation

We treated a 39‐year‐old woman with hypoproteinemia and anemia who had profuse gastric polyposis. Radiographic and endoscopic examination showed numerous polyps restricted to the stomach. The patient had pulmonary arteriovenous malformations in the left lung. Histological examination of the resected stomach revealed the gastric polyposis to be composed of cystic dilatation of the glands with small areas of adenocarcinoma. These findings were compatible with gastric juvenile polyposis (GJP) accompanied by gastric cancer. Analysis of genomic DNA revealed that the patient had truncating mutation of SMAD4, a responsible gene for juvenile polyposis (JP). Our case suggests that SMAD4 is possibly a responsible gene for GJP. © 2005 Wiley‐Liss, Inc.
Reported sexually transmitted disease clinic attendance and sexually transmitted infections in britain: prevalence, risk factors, and proportionate population burden.

BACKGROUND We examined attendance at sexually transmitted disease (STD) clinics and the prevalence, distribution, and associated demographic and behavioral factors of self-reported sexually transmitted infections (STIs) in a population survey of sexual attitudes and lifestyles. METHODS We analyzed data from stratified probability sample surveys obtained through the British National Surveys of Sexual Attitudes and Lifestyles (Natsal), which was undertaken in 1990 (n=13,765) and 2000 (n=11,161) among men and women aged 16-44 years. National STD surveillance data for 1999 were used to determine disease- and risk factor-specific proportionate population burden (PPB). RESULTS Between 1990 and 2000, the number of subjects who reported having attended an STD clinic during the past 5 years increased from 4.3% to 7.6% among men and from 3.3% to 6.6% among women. In 2000, 3.0% of men and 4.0% of women reported having received a diagnosis of an STI during the past 5 years; 77.6% of men and 60.3% of women with an STI had attended an STD clinic. Reported STI acquisition was independently associated with age, increasing numbers of sex partners, male homosexual partners, and partners from abroad (for women only). Of all reported STIs during the past 5 years (PPB, 10.2%), 10.2% were reported by the 2.9% of men who reported having had homosexual partners during the past 5 years. Of all reported STIs in the past 5 years (PPB, 41.6%), 41.6% were reported by the 4.0% of women who reported having > or =10 sex partners during that time. Analysis of national STI surveillance data showed that the PPB for new episodes of Chlamydia trachomatis diagnosed among homosexual men was 2.8%, that for gonorrhea was 17.4%, and that for syphilis was 32.1%. CONCLUSIONS Numbers and types of sexual partnerships remain the dominant individual and population risk factors for STI acquisition. Combined population behavior and surveillance data demonstrate the high PPB for STIs attributable to key risk factors. PPB may be a useful indicator of epidemic "phase" and may help target resources and guide prevention strategies.
Projections from bed nuclei of the stria terminalis, anteromedial area: Cerebral hemisphere integration of neuroendocrine, autonomic, and behavioral aspects of energy balance

The anteromedial area of the bed nuclei of the stria terminalis (BSTam) is the relatively undifferentiated region of the anterior medial (anteromedial) group of the bed nuclei of the stria terminalis (BSTamg), which also includes the more distinct dorsomedial, magnocellular, and ventral nuclei. The overall pattern of axonal projections from the rat BSTam was analyzed with the Phaseolus vulgaris‐leucoagglutinin anterograde pathway tracing method. Brain areas receiving relatively moderate to strong inputs from the BSTam fall into five general categories: neuroendocrine system (regions containing pools of magnocellular oxytocin neurons, and parvicellular corticotropin‐releasing hormone, thyrotropin‐releasing hormone, somatostatin, and dopamine neurons); central autonomic control network (central amygdalar nucleus, descending paraventricular nucleus, and ventrolateral periaqueductal gray); hypothalamic visceromotor pattern generator network (five of six known components); behavior control column (descending paraventricular nucleus and associated arcuate nucleus; ventral tegmental area and associated nucleus accumbens and substantia innominata); and behavioral state control (supramammillary and tuberomammillary nuclei). The BSTam projects lightly to thalamocortical feedback loops (via the medial‐midline‐intralaminar thalamus). Its pattern of axonal projections, combined with its pattern of neural inputs (the most varied of all BST cell groups), suggests that the BSTam is part of a striatopallidal differentiation involved in coordinating neuroendocrine, autonomic, and behavioral or somatic responses associated with maintaining energy balance homeostasis. J. Comp. Neurol. 494:142–178, 2006. © 2005 Wiley‐Liss, Inc.
NXT1 (p15) Is a Crucial Cellular Cofactor in TAP-Dependent Export of Intron-Containing RNA in Mammalian Cells

ABSTRACT TAP, the human homologue of the yeast protein Mex67p, has been proposed to serve a role in mRNA export in mammalian cells. We have examined the ability of TAP to mediate export of Rev response element (RRE)-containing human immunodeficiency virus (HIV) RNA, a well-characterized export substrate in mammalian cells. To do this, the TAP gene was fused in frame to either RevM10 or RevΔ78–79. These proteins are nonfunctional Rev mutant proteins that can bind to HIV RNA containing the RRE in vivo but are unable to mediate the export of this RNA to the cytoplasm. However, the fusion of TAP to either of these mutant proteins gave rise to chimeric proteins that were able to complement Rev function. Significantly, cotransfection with a vector expressing NXT1 (p15), an NTF2-related cellular factor that binds to TAP, led to dramatic enhancement of the ability of the chimeric proteins to mediate RNA export. Mutant-protein analysis demonstrated that the domain necessary for nuclear export mapped to the C-terminal region of TAP and required the domain that interacts with NXT1, as well as the region that has been shown to interact with nucleoporins. RevM10-TAP function was leptomycin B insensitive. In contrast, the function of this protein was inhibited by ΔCAN, a protein consisting of part of the FG repeat domain of CAN/Nup214. These results show that TAP can complement Rev nuclear export signal function and redirect the export of intron-containing RNA to a CRM1-independent pathway. These experiments support the role of TAP as an RNA export factor in mammalian cells. In addition, they indicate that NXT1 serves as a crucial cellular cofactor in this process.
Changes in exhaled nitric oxide related to estrogen and progesterone during the menstrual cycle.

BACKGROUND Significant changes in asthma and atopy occur throughout the menstrual cycle. We hypothesized that the characteristics of asthma (eg, symptoms, exhaled nitric oxide [eNO] levels as a marker of airway inflammation, pulmonary function, and atopy) vary throughout the menstrual cycle in relation to changes in the levels of estrogen or progesterone and that this variation is attenuated in women using oral contraception (OC). METHODS Seventeen women with asthma were studied over the course of their menstrual cycle through daily measurements of symptoms, eNO, spirometry, 17beta-estradiol, and progesterone levels, and through the performance of alternate-day allergy skin-prick tests (SPTs). RESULTS Of 534 potential daily visits, 526 (98.5%) were completed. Women not using OC (n = 8) had higher mean eNO levels (48.2 parts per billion [ppb]; 95% CI, 43.1 ppb to 53.3 ppb) than women using OC (27.0 ppb; 95% CI, 24.2 ppb to 29.7 ppb; p <or= 0.005). Among women not using OC, a 10 pmol/L increase in 17beta-estradiol levels was associated with a 15.2-ppm decrease in eNO levels (95% CI, -23.4 ppb to -7.0 ppm; p < 0.005). In contrast, an increase in progesterone level of 0.5 nmol/L was significantly associated with a 10.0-ppb increase in eNO (95% CI, 1.2 ppb to 18.7 ppb; p <or= 0.05). Consistent and significant results were found for 17beta-estradiol and progesterone levels and SPT. There were no significant associations between sex hormones and markers of asthma among women using OC. CONCLUSION During natural menstrual cycles, increases in estrogen levels were associated with decreased eNO levels, whereas increases in progesterone levels were associated with increased eNO levels and SPT wheal size. These effects were not observed among women using OC.