Miracle-dz/UniFAR-FTUs huggingface dataset:
A genetic linkage map for the domesticated silkworm, Bombyx mori , based on restriction fragment length polymorphisms

We present data for the initial construction of a molecular linkage map for the domesticated silkworm, Bombyx mori , based on 52 progeny from an F2 cross from a pair mating of inbred strains p50 and C108, using restriction fragment length polymorphisms (RFLPs). The map contains 15 characterized single copy sequences, 36 anonymous sequences derived from a follicular cDNA library, and 10 loci corresponding to a low copy number retrotransposon, mag. The 15 linkage groups and 8 ungrouped loci account for 23 of the 28 chromosomes and span a total recombination length of 413 cM; 10 linkage groups were correlated with established classic genetic maps. Scoring data from Southern blots were analysed using two Pascal programs written specifically to analyse linkage data in Lepidoptera, where females are the heterogametic sex and have achiasmatic meiosis (no crossing-over). These first examine evidence for linkage by calculating the maximum lod score under the hypothesis that the two loci are linked over the likelihood under the hypothesis that the two loci assort independently, and then determine multilocus linkage maps for groups of putatively syntenic loci by calculating the maximum likelihood estimate of the recombination fractions and the log likelihood using the EM algorithm for a specified order of loci along the chromosome. In addition, the possibility of spurious linkage was exhaustively tested by searching for genotypes forbidden by the absence of crossing-over in one sex.
Skeletal muscle expression analysis of fat metabolism genes in pig

Abstract Fat content and backfat thickness are important polygenic parameters influencing meat quality and carcass traits in pigs. Up to now, there is a lack of knowledge on the expression level of the genes encoding for enzymes involved in fatty acid metabolism in porcine skeletal muscle. In the present study we analysed, by quantitative real time PCR, the expression of three genes, acetyl-CoA carboxylase (ACACA), ATP citrate lyase (ACL) and fatty acid synthase (FASN) in skeletal muscle tissue samples of Italian Large White and Italian Duroc pigs with divergent breeding values for backfat thickness or visible intramuscular fat. Significant differences of the expression level for ACACA gene (P=0.04) and for ACL gene (P=0.02) were observed between the two breeds, comparing the samples selected for backfat thickness trait. The expression analysis of FASN gene in the samples with different genotype at the SNP c.265C>T showed that the TT genotype presented the lowest values in both breeds. The differences observed between breeds should be further considered to investigate the putative involvement of these genes on fat deposition traits.
Serological variability among European isolates of radish mosaic virus

Serological variability of radish mosaic virus (RaMV) isolates from white mustard, winter turnip rape, Camelina sativa and Chinese cabbage, collected in the Czech Republic and Russia, was studied using antisera against the Czech isolate RaMV1. In contrast to previous studies, reasonable serological differences were found between isolates from different locations and hosts, and even between neighbouring mustard plants in the field. Serological variability of European isolates was confirmed in extended experiments involving an Italian isolate, the American Type Strain (ATS) and its homologous antiserum. The results indicate that, in Europe, RaMV isolates may occur which differ both serologically and in host plant response, but no typical strains can be defined with the methods and isolates employed so far. Camelina sativa is reported as a new host of the virus.
Comparison of Peptidic and Nonpeptidic δ-Opioid Agonists on Guanosine 5′-O-(3-[35S]thio)triphosphate ([35S]GTPγS) Binding in Brain Slices from Sprague-Dawley Rats

Previous studies have demonstrated that peptidic and nonpeptidic δ-opioid receptor agonists have different effects depending on the measure. For example, nonpeptidic δ-opioid agonists, but not peptidic agonists, produce convulsions in rats, and in vitro studies suggested that peptidic and nonpeptidic δ-opioid agonists might have differential mechanisms of receptor downregulation. The present study evaluated potential differences between peptidic and nonpeptidic δ-opioid agonists in their ability to activate G proteins using guanosine 5′-O-(3-[35S]thio)triphosphate ([35S]GTPγS) autoradiography experiments in rat brain slices. The peptidic agonist [d-Pen2,d-Pen5]-enkephalin and the nonpeptidic agonist (+)BW373U86 [(+)-4-[α(R)-α-[(2S,5R)-2,5-dimethyl-4-(2-propenyl)-1-piperazinyl]-(3-hydroxyphenyl)methyl]-N,N-diethylbenzamide] demonstrated concentration-dependent increases in [35S]GTPγS binding that were attenuated by the δ-opioid antagonist naltrindole. (+)BW373U86 was more potent and efficacious than the peptidic agonist, and this difference remained consistent across brain regions where significant stimulation was observed. In addition, multiple δ-opioid compounds were evaluated for their agonist activity in this assay. These data suggested that differences between peptidic and nonpeptidic δ-opioid agonists in behavioral studies were most likely caused by differences in agonist efficacy. Finally, these data also revealed that [35S]GTPγS autoradiography could be used to compare efficacy differences among agonists across various brain regions in rat brain slices.
Asymmetric high-order anatomical brain connectivity sculpts effective connectivity

Abstract Bridging the gap between symmetric, direct white matter brain connectivity and neural dynamics that are often asymmetric and polysynaptic may offer insights into brain architecture, but this remains an unresolved challenge in neuroscience. Here, we used the graph Laplacian matrix to simulate symmetric and asymmetric high-order diffusion processes akin to particles spreading through white matter pathways. The simulated indirect structural connectivity outperformed direct as well as absent anatomical information in sculpting effective connectivity, a measure of causal and directed brain dynamics. Crucially, an asymmetric diffusion process determined by the sensitivity of the network nodes to their afferents best predicted effective connectivity. The outcome is consistent with brain regions adapting to maintain their sensitivity to inputs within a dynamic range. Asymmetric network communication models offer a promising perspective for understanding the relationship between structural and functional brain connectomes, both in normalcy and neuropsychiatric conditions.
Mercury-induced changes in growth variables and antioxidative enzyme activities in Indian mustard

Abstract In a hydroponic system, experiments were conducted to study the effect of different levels of mercury treatments (0, 5, 10, 25 and 50 µM Hg) on Indian mustard (Brassica juncea L. Czern & Coss.) cv. Pusa Jai Kisan. Concentration-dependent inhibitory effects were observed on growth characteristics (plant dry mass, leaf area, shoot and root length). These were accompanied by an increase in shoot Hg content and in oxidative stress characteristics such as the MDA and H2O2 levels. The plant growth decreased maximally at 50 µM of Hg. Despite a reduction in growth, activities of antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR) were enhanced with increase in Hg-treatments. The Hg-induced alterations in growth are linked with increase in lipid peroxidation (MDA and H2O2), whereas the enhancement in activities of antioxidant enzymes protects plants from Hg-induced oxidative stress.
Fluorescein-agarose gel as a tissue model to visualize and measure local CAP-induced acidification

Cold Atmospheric Plasmas (CAPs) have been shown to lower the pH of the treated target. CAP-induced acidification can have beneficial effects on the treated tissue (e.g. disinfection and healing). Conversely a tissue hyper acidification can lead to permanent damages with dramatic consequences. Before starting in vivo plasma treatments, preliminary tests should be carried in order to tune the acidifying effect induced by CAP exposition. Here we propose a tissue model that can be a useful tool to visualize and measure pH changes induced by plasma treatment.
Photoaged Skin Therapy with Adipose-Derived Stem Cells

Supplemental Digital Content is available in the text. Background: The major intrinsic cause of facial skin degeneration is age, associated with extrinsic factors such as exposure to sun. Its major pathologic causes are degeneration of the elastin matrix, with loss of oxytalan and elaunin fibers in the subepidermal region, and actinic degeneration of elastin fibers that lose their functional properties in the deep dermis. Therapy using autologous adipose mesenchymal stem cells for regeneration of extracellular matrix in patients with solar elastosis was addressed in qualitative and quantitative analyses of the dermal elastic fiber system and the associated cells. Methods: Mesenchymal stem cells were obtained from lipoaspirates, expanded in vitro, and introduced into the facial skin of patients submitted after 3 to 4 months to a face-lift operation. In the retrieved skin, immunocytochemical analyses quantified elastic matrix components; cathepsin K; matrix metalloproteinase 12 (macrophage metalloelastase); and the macrophage M2 markers CD68, CD206, and hemeoxygenase-1. Results: A full de novo formation of oxytalan and elaunin fibers was observed in the subepidermal region, with reconstitution of the papillary structure of the dermal-epidermal junction. Elastotic deposits in the deep dermis were substituted by a normal elastin fiber network. The coordinated removal of the pathologic deposits and their substitution by the normal ones was concomitant with activation of cathepsin K and matrix metalloproteinase 12, and with expansion of the M2 macrophage infiltration. Conclusion: The full regeneration of solar elastosis was obtained by injection of in vitro expanded autologous adipose mesenchymal stem cells, which are appropriate, competent, and sufficient to elicit the full structural regeneration of the sun-aged skin. CLINICAL QUESTION/LEVEL OF EVIDENCE: Therapeutic, IV.
Neurofilament Proteins in Goldfish Optic Axons a

The premier model of axonal regeneration in the CNS of vertebrate animals is the retino-tectal pathway in ray-finned fishes. Within two months after transecting the optic nerves in goldfish, there is a recovery of visual acuity, color vision, and visual fields that approximates the normal condition. Axonal outgrowth begins within five days, and axonal elongation proceeds at 0.3 to 0.4 mm/day. * Axons reach the contralateral optic tectum and begin to form synapses by the end of the third week? Since neurofilaments and microtubules stabilize the shape of the outgrowing axon, it is important to characterize the axonal transport of tubulin and the neurofilament proteins in attempting to account for the remarkable regenerative capacity of these axons. In mammalian retinal ganglion cells, these proteins advance with the slowest of the three major rate-components of anterograde axonal transport, slow component a or This is thought to represent the movement of the microtubule-neurofilament network, since the peaks of labeling for tubulin and the neurofilament triplet are cotransported. In mammalian motoneurons, however, tubulin travels with the next faster rate-component (SCb) as well as SCa," so that SCa is defined by the movement of labeled neurofilament protein^. ^ In goldfish retinal ganglion cells, most of the labeled tubulin advances at 0.4-0.7 m m / d a ~ , ~ . ~ but SCa has yet to be defined because the neurofilament proteins have not been fully characterized. To identify neurofilament proteins, cytoskeletal fractions were prepared from goldfish optic nerves by Triton X-100 extraction. Proteins were separated by SDSpolyacrylamide gel electrophoresis (SDS-PAGE), and presumptive neurofilament proteins were detected on the basis of reactivity with Bodian's silver stain,' antibodies against mammalian neurofilament proteins (aNF),8 and a monoclonal antibody against an epitope common to all intermediate filament proteins (aIF)? Each of these markers reacted with polypeptides having SDS-molecular weights of 135K, 80K, and 58-60K. Further identification was obtained by immunoblotting after separating polypeptides by using two-dimensional PAGE. Both aIF and aNF reacted with polypeptides
Methylation Status of the Retinoblastoma Gene (RB1) in Osteosarcoma: No Evidence for Hypermethylation

Alterations of the retinoblastoma (RB1) tumor suppressor gene are not only associated with retinoblastoma but also with several other malignancies including osteosarcoma. Besides direct sequence alterations, hypermethylation of a CpG island in the promoter region can cause inactivation of the RB1 gene as it has been shown in retinoblastomas. We examined the methylation status of the RB1 gene in 25 osteosarcoma specimens by using the methylation-sensitive restriction enzymes SacII and SmaI. The restriction fragments were hybridized with clone p123, which is a 1.8-kb genomic subclone that spans the RB1 CpG island including the promoter region and exon 1. Whereas we reconfirmed hypermethylation of the RB1 gene in a sporadic retinoblastoma, no hypermethylation could be detected in the 25 osteosarcoma specimens, suggesting that hypermethylation of the RB1 promoter is not of major importance during osteosarcoma genesis.
Evolutionary Origins of The Mammalian Promontorium and Cochlea

ABSTRACT Mammals have two apomorphies in the ear region: an elongated cochlear canal and an eminence on the tympanic side of the cochlear housing, known as the petrosal promontorium. In nonmammalian cynodonts, the cochlear recess is shorter, smaller, and oriented more medially than the mammalian cochlear canal; their cochlear housing is formed by the prootic, opisthotic, and basisphenoid. New fossil materials of two early mammals, Adelobasileus and Sinoconodon, reveal evidence on the evolutionary transformation of the mammalian cochlear canal and bony cochlear housing. Adelobasileus is more derived than any known non-mammalian cynodont in possessing an incipient promontorium, but more primitive than other mammals in retaining a vestigial basisphenoid wing. Sinoconodon has a fully developed petrosal promontorium but a short cochlea that extends only one third of the promontorium length. The cochlear canal of Morganucodon is twice as long as that of Sinoconodon, relative to both skull and promontorium. More.
Effect of High-Dose Growth Hormone and Glutamine on Body Composition, Urine Creatinine Excretion, Fatty Acid Absorption, and Essential Fatty Acids Status in Short Bowel Patients. A Randomized, Double-blind, Crossover, Placebo-controlled Study

Background: Positive effects of high dose growth hormone and glutamine (GH + GLN) on body composition in short bowel patients have been described. Lack of effects on intestinal absorption found in some studies has been ascribed to concomitant essential fatty acid (EFA) deficiency. This study describes changes in body weight (BW) and composition, 24-h urine creatinine excretion, intestinal fatty acid absorption (total, saturated, unsaturated and EFA), and EFA status in relation to treatment with GH + GLN in 8 short bowel patients. Methods: A double-blind, crossover study between placebo and growth hormone (mean, 0.12 mg/kg/day) plus oral (mean, 28 g/day) and parenteral glutamine (mean, 5.2 g/day) for 28 days. Body composition was measured by dual-energy absorptiometry (DEXA) scans. Intestinal fatty acid absorption was evaluated in balance studies, and EFAs were measured in plasma phospholipids by gas liquid chromatography. Results: Active treatment did not increase BW, lean body mass (LBM), fat mass (FM) and bone mass significantly compared with placebo treatment, but BW increased 1.03 kg (1.7%, P < 0.05), LBM 2.93 kg (8.7%, P < 0.001) and FM decreased 2.41 kg (10.6%, P < 0.001) in comparison with baseline. Twenty-four-hour urine creatinine excretion did not differ between study periods. No changes in intestinal absorption of fatty acids were seen, and no changes in EFAs measured in plasma phospholipids were observed. Only 1 of 8 patients, who did not receive parenteral lipids, had a Holman index above 0.2, indicative of EFA deficiency. All developed peripheral oedema. Conclusions: Combined high dose growth hormone and glutamine administered for 4 weeks, did not improve absorption of fatty acids or EFA status in short bowel patients. No changes in BW or composition were seen when comparing treatment to placebo periods. The increase in LBM measured by DEXA scan, comparing treatment and baseline periods, was not accompanied by an increase in the 24-h urinary creatinine excretion and is suspected to be associated with an accumulation in extracellular fluids.
Male Breast Cancer?A Reappraisal of Clinical and Biologic Indicators of Prognosis

Between 1970 and 1998, 90 cases of male breast cancer with available pathological material were retrieved. The disease often presented in aged patients (median? 66 years) and as advanced stage (stage III/IV? 51%). Excluding stage IV disease, the neoplasia were predominantly ductal invasive carcinomas, NOS (not otherwise specified) (92%), grade 1 and grade 2 (94%), positive for estrogen and progesterone receptors (72% and 74%), negative for androgen receptors (100%), p53 negative (95%), c-erbB-2 negative (88%) and DNA aneuploid (73%). Assessment of disease outcome is determined by stage at time of diagnosis, and axillary lymph node status was the only parameter found to have a statistically significant correlation with either disease-free interval or overall survival (p < 0.001) by multivariate analysis. Clinically useful information on the probability of relapse can be added by determining c-erbB-2 (p = 0.02) and progesterone receptors (p = 0.04) in stage III and tumor ploidy (p = 0.04) in pN1 subgroups of patients.
Effect of a Lacto-ovo Vegetarian Diet on Fasting Small Intestinal Motility

Background: Changes in diet can alter gastric and small intestinal (SI) motility. The effects of a vegetarian diet on fasting SI motility are unknown. Methods: Manometric studies were performed in 9 lacto-ovo vegetarians (7 women) and 9 omnivores (7 women) of similar age and body mass index. On each study day, manometry was used to assess SI motility for 5 h, or 3 complete cycles of the interdigestive motor complex (IDMC). Lacto-ovo vegetarians were studied once; omnivores were studied twice, on their usual diet, and after consuming a 14-day lacto-ovo vegetarian diet. Diet diaries were kept for 5 days prior to each manometric study. Data were analysed for dietary composition and for cycle length and duration of each phase (I, II and III) of the IDMC. Results:
Cost-effectiveness of Interferon Alfa-2b With and Without Ribavirin as Therapy for Chronic Hepatitis C in Sweden

Background: Recent trials have shown that treatment with a combination of interferon alfa-2b and ribavirin results in sustained loss of detectable hepatitis C-virus (HCV) RNA in a higher proportion of patients than treatment with interferon alone. Combination therapy, however, is two to three times as expensive as monotherapy. Methods: Based on data from recent randomized clinical trials and a previously published decision model, we developed a Markov model to estimate the cost-effectiveness of initial combination therapy with interferon and ribavirin versus interferon alone for previously untreated patients with chronic HCV infection in Sweden. Clinical praxis and quality adjustments were based on expert estimates and costs were gathered from different health care providers in Sweden. Results: Combination therapy for 24 or 48 weeks, compared to interferon alone, prolonged quality adjusted life expectancy by 0.5 to 1.1 years at marginal cost-effectiveness ratios of US$ 1,400 to US$ 6,000 per DQALY (discounted quality-adjusted life-year) for patients with genotype 1. In genotype 1, 48 weeks compared to 24 weeks of combination therapy prolonged quality adjusted life expectancy by 0.6 years at a marginal cost-effectiveness ratio of $US 9,800 per DQALY. For patients with genotype non-1, combination therapy for 24 or 48 weeks, compared to interferon alone, prolonged quality adjusted life expectancy by 2.3 years, with combination therapy for 24 weeks being money-saving. The results were robust in sensitivity analyses. Conclusion: Combination therapy with interferon and ribavirin increased quality-adjusted life expectancy and was cost-effective for patients with chronic hepatitis C.
Incomplete Remission with Short-Term Prednisolone Treatment in Collagenous Colitis: a Randomized Study

Background: Microscopic colitis is a disease of unknown aetiology characterized by chronic watery diarrhoea and diarrhoea can be eliminated by budesonide but frequently recurs when budesonide is stopped. We studied whether prednisolone could induce remission in patients with disabling, chronic diarrhoea due to microscopic colitis. Methods: A double-blind, randomized (3:1) trial of oral prednisolone 50 r mg daily or placebo for 2 weeks. Remission was defined as stool weight h 200 r g/day or frequency h 2/day; effect was defined as >50% reduction of either stool frequency or weight. Six centres screened 31 consecutive patients and included 11 with collagenous colitis and 1 with lymphocytic colitis. Median duration of diarrhoea was 9 months. Patients had a normal colonoscopy, and no evidence of coeliac disease, bile acid or lactose malabsorption. Patients with gastrointestinal infection, previous gastrointestinal surgery, abnormal biochemical screening or recent treatment with immunosuppressive agents were excluded. Results: Stool weight (grams) declined in 7 of 9 patients given prednisolone and in 1 of 3 receiving placebo; changes in median weight were from 430 to 278 and from 825 to 489, respectively. Stool frequency (per day) declined from 6 to 3 and from 8 to 5. Remission was obtained in 2 and 0, and effect in 5 and 0, respectively (NS; Fisher exact test). Conclusions: Prednisolone 50 r mg daily for 2 weeks induces incomplete remission in patients with chronic diarrhoea due to collagenous colitis.
Isolation and Characterization of Flavobacterium johnsoniae from Farmed Rainbow Trout Oncorhynchus mykiss

Flavobacterium johnsoniae was isolated from farmed rainbow trout Oncorhynchus mykiss in Korea, and its biochemical and molecular characterization was determined. Yellow-pigmented bacterial colonies were isolated from 18 of 64 fish samples (28.1%) on trypticase soy agar plates, and their biochemical profiles were characterized by API 20E and API 20NE test kits. F. johnsoniae was identified by biochemical phenotyping of factors including rapid gliding motility, Gram-negative condition, oxidase- and catalase-positive status, Congo red absorption, nitrate reduction, -galactosidase production, acid production from glucose, and gelatin and casein hydrolysis. PCR and subsequent sequencing of 16S rRNA confirmed that the yellow-pigmented colonies were most similar to F. johnsoniae. The alignment analysis of 16S rRNA sequences also showed that all 18 rainbow trout isolates had highly similar homologies (97-99% identity). One isolate was selected and named FjRt09. This isolate showed 98% homology with previously reported F. johnsoniae isolates, and in phylogenetic analysis was more closely grouped with F. johnsoniae than with F. psychrophilum, F. columnare, or F. branchiophilum. This is the first report on the occurrence and biochemical characterization of F. johnsoniae isolated from rainbow trout in Korea.