Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance evaluation of the multi-device OpenCL FDTD solver

We present results of an evaluation of a multi-device OpenCL FDTD solver. Portability between hardware manufactured by different vendors and also between highly specialized and parallel computing architectures available on the market, i.e. GPUs, multi-core CPUs and devices integrating both technologies in a single-die IC, is the main advantage of this solver. For code execution on GPUs, the computational domain is decomposed along the slowest direction, and electromagnetic field boundary data is shared between neighboring subdomains. The communication overhead between GPUs is proportional to the area of the boundary and represents the rate-limiting step of the method. Utilized hardware devices allow the communication overhead to be hidden by computations for sufficiently large simulation domains, giving a scaling efficiency higher than 90%. CPUs placed in different sockets on a motherboard are visible by the OpenCL driver as a single computing device with an aggregated number of cores, thus decomposition of the domain is not necessary for solver execution on multi-core CPUs. The paper subsequently shows results of numerical tests aimed at evaluation of the developed code in realistic simulations of problems in computational electromagnetics.
Antioxidant and antimicrobial activities of branches extracts of five Juniperus species from Turkey

Context: Several Juniperus species (Cupressaceae) are utilized in folk medicine in the treatment of infections and skin diseases. Objective: This work was designed to evaluate the antioxidant and antimicrobial potential of methanol and water branches extracts of Juniperus species from Turkey: Juniperus communis L. var. communis (Jcc), Juniperus communis L. var. saxatilis Pall. (Jcs), Juniperus drupacea Labill. (Jd), Juniperus oxycedrus L. subsp. oxycedrus (Joo), Juniperus oxycedrus L. subsp. macrocarpa (Sibth. & Sm.) Ball. (Jom). Materials and methods: Total phenolics, total flavonoids and condensed tannins were spectrophotometrically determined. The antioxidant properties were examined using different in vitro systems. The toxicity was assayed by Artemia salina lethality test. The antimicrobial potential against bacteria and yeasts was evaluated using minimum inhibitory concentration and minimum bactericidal concentration (MIC/MBC) measurements. The effect on bacteria biofilms was tested by microtiter plate assay. Results: Both in the DPPH (1,1-diphenyl-2-picrylhydrazyl) and TBA (thiobarbituric acid) test Jom resulted the most active (IC50 = 0.034 ± 0.002 mg/mL and 0.287 ± 0.166 µg/mL). Joo exhibited the highest reducing power (1.78 ± 0.04 ASE/mL) and Fe2+ chelating activity (IC50 = 0.537 ± 0.006 mg/mL). A positive correlation between primary antioxidant activity and phenolic content was found. The extracts were potentially non-toxic against Artemia salina. They showed the best antimicrobial (MIC = 4.88-30.10 µg/mL) and anti-biofilm activity (60–84%) against S. aureus. Discussion and conclusion: The results give a scientific basis to the traditional utilization of these Juniperus species, also demonstrating their potential as sources of natural antioxidant and antimicrobial compounds.
Retinoic acid stimulates the transcription of insulin‐like growth factor binding protein‐6 in skeletal cells

Retinoic acid has important actions on cell differentiation and osteoblastic function, and some of these actions may be mediated by changes in the insulin‐like growth factor (IGF) axis. Skeletal cells synthesize IGF I and II and the six known IGF binding proteins (IGFBP). IGFBP‐6 binds IGF II with high affinity and prevents IGF II‐mediated effects. In fibroblasts, IGFBP‐6 levels are regulated by retinoic acid, and we postulated that retinoic acid may regulate IGF II in bone by altering IGFBP‐6 synthesis. We examined the effect of retinoic acid on IGFBP‐6 expression in cultures of osteoblast‐enriched cells from 22‐day fetal rat calvariae (Ob cells). Retinoic acid caused a time‐ and dose‐dependent increase in IGFBP‐6 mRNA levels, as determined by Northern blot analysis. The effect was maximal after 48 h of treatment and observed with retinoic acid at concentrations of 10 nM to 1 μM. Retinoic acid increased IGFBP‐6 polypeptide levels in the culture medium, as determined by Western immunoblot analysis. Cycloheximide at 3.6 μM slightly decreased IGFBP‐6 transcripts but did not prevent the stimulatory effect of retinoic acid. The decay of IGFBP‐6 mRNA in transcriptionally arrested Ob cells was similar in control and retinoic acid‐treated cells, and retinoic acid increased the rates of IGFBP‐6 transcription, as determined by nuclear run on assays. In conclusion, retinoic acid enhances IGFBP‐6 expression in Ob cells by transcriptional mechanisms. Since IGFBP‐6 prevents the effects of IGF II, increased synthesis of IGFBP‐6 could mediate selected actions of retinoic acid in bone. © 1996 Wiley‐Liss, Inc.
Evaluation of Nutritional Status and Factors Related to Malnutrition in Children on CAPD

Objective The aim of this study was to investigate the nutritional status of children on continuous ambulatory peritoneal dialysis (CAPD) and to relate it to the dose of dialysis and serum levels of inflammatory cytokines and insulin-like growth factor-1 (IGF-1). Patients 17 CAPD patients (8 girls, 9 boys; mean age 13.1 ± 3.5 years, median 15 years) were included in the study. Anthropometric measurements and serum albumin levels were used in the evaluation of nutritional status. Serum interleukin (IL)-1β, IL-6, tumor necrosis factor α, and IGF-1 levels were determined in all CAPD patients and in a healthy control group. Weekly Kt/V and creatinine clearance (CCr) were measured to determine adequacy of dialysis. Results The mean dialysis period was 23.7 ± 15.2 months (median 23 months). Anthropometric measurements and serum albumin level were as follows: height 130.2 ± 15.6 cm, height standard deviation score (HtSDS) -4.2 ± 2.4, body mass index (BMI) 16.3 ± 1.6 kg/m2, body mass index standard deviation score (BMISDS) -0.8 ± 0.9, triceps skinfold thickness (TST) 4.2 ± 1.4 mm, midarm circumference (MAC) 16.21 ± 2.3 cm, upper arm muscle area (AMA) 1799.1 ± 535.7 mm2, upper arm fat area (AFA) 334.5 ± 143 mm2, and serum albumin 3.1 ± 0.7 g/dL. The BMI was above the fifth percentile in all patients; TST and MAC were below the fifth percentile in 14 patients (82.4%) and 10 patients (58.8%) respectively. The AMA was below the fifth percentile in 8 patients; however, the AFA was below the fifth percentile in all patients. Mean serum albumin level was under 3.5 g/dL in 70.5% of the children. We found significant positive correlations between BMI and Kt/V (r = 0.69, p < 0.01), CCr (r = 0.64, p < 0.05), and IL-6 (r = 0.61, p < 0.01). There was an inverse correlation between BMISDS and dialysis period (r = -0.58, p < 0.05); and between IL-6 and serum albumin (r = -0.49, p < 0.05). A significant positive correlation between BMISDS and serum IGF-1 level (r = 0.62, p < 0.01) was noted. We also found a significant positive correlation between serum IGF-1 level and both HtSDS (r = 0.57, p < 0.05) and TST (r = 0.52, p < 0.05). Significant positive correlations between AFA and CCr and IGF-1 were also noted (both r = 0.56, p < 0.05). Conclusion Although many factors may be responsible for malnutrition and growth retardation, we found that prolonged period of dialysis, inadequate dialysis, and low IGF-1 levels are the most important risk factors in CAPD patients.
Suprascapular Nerve Block for Ipsilateral Shoulder Pain After Thoracotomy with Thoracic Epidural Analgesia: A Double-Blind Comparison of 0.5% Bupivacaine and 0.9% Saline

Despite receiving thoracic epidural analgesia, severe ipsilateral shoulder pain is common in patients after thoracotomy. We recruited 44 patients into a double-blinded randomized placebo-controlled study to investigate whether suprascapular nerve block would treat postthoracotomy shoulder pain effectively. All patients received a standard anesthetic with a midthoracic epidural. Thirty patients who experienced shoulder pain within 2 h of surgery were randomly assigned to receive a suprascapular nerve block with either 10 mL of 0.5% bupivacaine or 10 mL of 0.9% saline. Shoulder pain was assessed before nerve blockade, at 30 min, and then hourly for 6 h after the block using a visual analog scale (VAS) and a 5-point verbal ranking score (VRS). The incidence of shoulder pain before nerve block was 78%. There was no significant decrease in either VAS or VRS in the Bupivacaine group. These results suggest that this pain is unlikely to originate in the shoulder and lead us to question the role of a somatic afferent in referred visceral pain. We conclude that suprascapular nerve block does not treat ipsilateral shoulder pain after thoracotomy in patients with an effective thoracic epidural.
Fertility and pregnancy outcome following pelvic arterial embolization for severe post-partum haemorrhage. A cohort study.

BACKGROUND Pelvic arterial embolization is a safe, effective life-saving procedure in post-partum haemorrhage, but little information is yet available about its impact on menstruation and fertility. METHODS A cohort of 28 women who underwent pelvic embolization for post-partum haemorrhage in our tertiary centre was studied. Patients were contacted by telephone to obtain long-term outcome for menstruation, clinical signs of estrogen insufficiency, desire for fertility and subsequent pregnancies. RESULTS We found no menstrual abnormalities or signs of early menopause among the 17 patients we were able to reach. Six women expressed a clear desire for subsequent pregnancies. Five patients reported a total of six pregnancies (one biochemical pregnancy, one early miscarriage and four deliveries). The four patients with complete gestations gave birth to healthy babies, but post-partum haemorrhage recurred for all and led to two hysterectomies. No undesired pregnancies occurred. CONCLUSIONS Embolization in post-partum haemorrhage appears to be a safe procedure that does not impair subsequent menstruation and fertility. Recurrence of severe post-partum haemorrhage may occur at subsequent deliveries.
The Effectiveness of Individualized Acupuncture Protocols in the Treatment of Gulf War Illness: A Pragmatic Randomized Clinical Trial

Background Gulf War Illness is a Complex Medical Illness characterized by multiple symptoms, including fatigue, sleep and mood disturbances, cognitive dysfunction, and musculoskeletal pain affecting veterans of the first Gulf War. No standard of care treatment exists. Methods This pragmatic Randomized Clinical Trial tested the effects of individualized acupuncture treatments offered in extant acupuncture practices in the community; practitioners had at least 5 years of experience plus additional training provided by the study. Veterans with diagnosed symptoms of Gulf War Illness were randomized to either six months of biweekly acupuncture treatments (group 1, n = 52) or 2 months of waitlist followed by weekly acupuncture treatments (group 2, n = 52). Measurements were taken at baseline, 2, 4 and 6 months. The primary outcome is the SF-36 physical component scale score (SF-36P) and the secondary outcome is the McGill Pain scale. Results Of the 104 subjects who underwent randomization, 85 completed the protocol (82%). A clinically and statistically significant average improvement of 9.4 points (p = 0.03) in the SF-36P was observed for group 1 at month 6 compared to group 2, adjusting for baseline pain. The secondary outcome of McGill pain index produced similar results; at 6 months, group 1 was estimated to experience a reduction of approximately 3.6 points (p = 0.04) compared to group 2. Conclusions Individualized acupuncture treatment of sufficient dose appears to offer significant relief of physical disability and pain for veterans with Gulf War Illness. This work was supported by the Office of the Assistant Secretary of Defense for Health Affairs through the Gulf War Illness Research Program under Award No. W81XWH-09-2-0064. Opinions, interpretations, conclusions and recommendations are those of the author and are not necessarily endorsed by the Department of Defense. Trial Registration ClinicalTrials.gov NCT01305811
Automated gain schedule synthesis for missile systems

Gain schedule synthesis typically involves significant manual tuning to meet various time and frequency domain design specifications. This work explores how optimization may achieve automatic tuning for missile systems. Here, vertical acceleration command tracking is considered with closed loop control of the short period dynamics. Tracking is achieved with robust servomechanism design and linear quadratic regulation. Tuning the controller is posed as an optimization problem to meet command tracking requirements subject to multiple design constraints. Sequential quadratic programming is applied to the optimization problem and provides automated tuning for individual and batch runs of controllers. A successful strategy for initial guess selection in batch runs is proposed and its importance for efficient automation is shown. These results support the viability of optimization methods for automated gain schedule synthesis in missile systems.
Increased risk of hepatocellular carcinoma in patients with diabetes mellitus: A systematic review and meta‐analysis of cohort studies

In recent years, increasing evidence has suggested a strong association between diabetes mellitus (DM) and hepatocellular carcinoma (HCC). To provide a quantitative assessment of this association, we performed a systematic review and meta‐analysis of cohort studies. We collected studies through a literature search of Medline from January 1, 1966 and EMBASE from January 1, 1974, through July 31, 2010. Summary relative risks (SRRs) with their corresponding 95% confidence intervals (CIs) were calculated using a random‐effects model. A total of 25 cohort studies that met our inclusion and exclusion criteria were included in our analysis. Among these, 18 studies showed that DM was associated with an increased incidence of HCC (SRRs = 2.01, 95% CI: 1.61–2.51), compared with individuals without DM. There was a statistically significant heterogeneity among these studies (Q = 136.68, p < 0.001, I2 = 87.6%). Analyses subgrouped by controlling confounders revealed that the increased incidence of HCC was independent of geographic location, alcohol consumption, history of cirrhosis, or infections with hepatitis B (HBV) or hepatitis C virus (HCV). In addition, DM was also positively associated with HCC mortality (SRR = 1.56; 95% CI: 1.30–1.87), with no significant evidence of heterogeneity among studies (Q = 1.16, p = 0.56, I2 =0%). There were no significant publication bias (p = 0.79 for Egger's regression asymmetry test). These findings strongly support a positive association between DM and increased risk of HCC in both males and females.
Chemotaxins inhibit neutrophil adherence to and transmigration across cytokine‐activated endothelium: Correlation to the expression of L‐selectin

Non‐activated neutrophils strongly adhere to cytokine‐activated human umbilical vein endothelial cells (HUVE). However, activation of neutrophils by different chemotactic mediators led to potent inhibition of this endothelial‐dependent interaction. For different formylated peptides, concentrations leading to maximal adherence inhibition coincided with those known for inducing maximal chemotactic migration of neutrophils. In terms of maximal adherence inhibition, a rank list was found in the order of N‐formyl‐Met‐Leu‐Phe > C5adesArg > interleukin‐8 > C5a ⩾ leukotriene B4, whereas platelet‐activating factor, and lipopolysaccharide showed no inhibition. This rank order was congruent to that of down‐regulation of neutrophil L‐selectin detected by the monoclonal antibody Leu‐8. Moreover, the dose‐dependent increase of neutrophil adherence inhibition corresponded to the loss of L‐selectin expression. Concentrations higher than that required for maximal inhibition led to a dose‐dependent decrease of inhibition, which was accompanied by increasing expression of neutrophil CD11/CD18. In contrast to the capacity of non‐activated neutrophils to migrate across interleukin‐1‐activated HUVE monolayers, transmigration was significantly impaired after chemotactic activation.
Functional significance of seminal receptacle length in Drosophila melanogaster

Abstract Despite its central role in post‐copulatory sexual selection, the female reproductive tract is poorly understood. Here we provide the first experimental study of the adaptive significance of variation in female sperm‐storage organ morphology. Using populations of Drosophila melanogaster artificially selected for longer or shorter seminal receptacles, we identify relationships between the length of this primary sperm‐storage organ and the number of sperm stored, pattern of progeny production, rate of egg fertilization, remating interval, and pattern of sperm precedence. Costs and benefits of relatively short or long organs were identified. Benefits of longer receptacles include increased sperm‐storage capacity and thus progeny production from a single insemination. Results suggest that longer receptacles have not naturally evolved because of developmental time costs and a correlated reduction in longevity of mated females. This latter cost may be a consequence of sexual conflict mediated by ejaculate toxicity. Receptacle length did not alter the pattern of sperm precedence, which is consistent with data on the co‐evolution of sperm and female receptacle length, and a pattern of differential male fertilization success being principally determined by the interaction between these male and female traits.
Maresin 1 ameliorates iron-deficient anemia in IL-10(-/-) mice with spontaneous colitis by the inhibition of hepcidin expression though the IL-6/STAT3 pathway.

BACKGROUND Approximately 50% of patients with inflammatory bowel disease (IBD) suffer from anemia, which is prevalently caused by iron deficiency. Maresin 1 (MaR1) is a novel docosahexaenoic acid-derived pro-resolving agent that promotes the resolution of inflammation. The aim of the present study was to investigate the therapeutic effects of MaR1 on iron-deficient anemia in IL-10 knockout (IL-10(-/-)) mice with spontaneous chronic colitis. METHODS IL-10(-/-) mice of 16 weeks of age with established colitis were used for the experiments with MaR1 treatment for 2 weeks. Histologic injury, CD4+ lymphocyte values in the lamina propria, blood hemoglobin, hematocrit, serum iron concentrations, transferrin saturation, splenic iron stores, levels of inflammatory cytokines, expression of liver hepcidin mRNA, and western blotting of STAT3 were analyzed in this study. RESULTS MaR1 treatment (0.3 ng/mouse) effectively attenuated histological colitis typically associated with decreased CD4+ lymphocytes in the lamina propria as well as the concentrations of MPO, TNF-α, IFN-γ, IL-6 and IL-17 (P<0.05). Furthermore, reduced expression of liver hepcidin mRNA and p-STAT3 expression, as well as increased hemoglobin concentration, hematocrit, levels of serum iron, transferrin saturation and splenic iron stores were found in IL-10(-/-) mice after MaR1 treatment (P<0.05). CONCLUSIONS These results indicate that MaR1 treatment ameliorates iron-deficient anemia by reducing colonic inflammation and inhibiting hepcidin expression though the IL-6/STAT3 pathway.
Routes of Acquisition of the Gut Microbiota of the Honey Bee Apis mellifera

ABSTRACT Studies of newly emerged Apis mellifera worker bees have demonstrated that their guts are colonized by a consistent core microbiota within several days of eclosure. We conducted experiments aimed at illuminating the transmission routes and spatiotemporal colonization dynamics of this microbiota. Experimental groups of newly emerged workers were maintained in cup cages and exposed to different potential transmission sources. Colonization patterns were evaluated using quantitative real-time PCR (qPCR) to assess community sizes and using deep sequencing of 16S rRNA gene amplicons to assess community composition. In addition, we monitored the establishment of the ileum and rectum communities within workers sampled over time from natural hive conditions. The study verified that workers initially lack gut bacteria and gain large characteristic communities in the ileum and rectum within 4 to 6 days within hives. Typical communities, resembling those of workers within hives, were established in the presence of nurse workers or nurse worker fecal material, and atypical communities of noncore or highly skewed compositions were established when workers were exposed only to oral trophallaxis or hive components (comb, honey, bee bread). The core species of Gram-negative bacteria, Snodgrassella alvi, Gilliamella apicola, and Frischella perrara, were dependent on the presence of nurses or hindgut material, whereas some Gram-positive species were more often transferred through exposure to hive components. These results indicate aspects of the colony life cycle and behavior that are key to the propagation of the characteristic honey bee gut microbiota.
Head and neck tumor sites differ in prevalence and spectrum of p53 alterations but these have limited prognostic value

The tumor site is a strong clinical factor in head and neck squamous cell carcinoma (HNSCC). To clarify the biologic and clinical role of p53 alterations in HNSCC, we have examined the prevalence and the nature of p53 alterations in a large cohort of tumors from the different sites. For immunohistochemical analysis of p53 protein expression, we introduced tyramide signal amplification immunohistochemistry (TSA‐IHC) on a tissue microarray. This allowed the discrimination between normal low‐level expression and reduced or lost expression. Two hundred fifty‐three tumors were subjected to mutational analysis by genomic DNA sequencing, employing also the p53 GeneChip from Affymetrix. The prevalence of all p53 alterations, i.e., mutations, overexpression and loss of expression, was significantly higher in hypopharyngeal tumors than in the other sites (p = 0.001). Laryngeal tumors showed the lowest rate of p53 alterations, but revealed a distinct mutation spectrum: most mutations affected exon 5 (p = 0.013) and the S2′ domain (p = 0.002), and most hot‐spot 248 mutations occurred in the larynx (p < 0.001). Sequencing by p53GeneChip technology was shown to be only insignificantly more sensitive than dideoxy sequencing. In agreement with p53 mutations occurring prior to invasiveness, their prevalence did not increase with tumor stage, and all mutation classes lacked prognostic significance. The large patient cohort of this study showed that p53 is differentially affected in the different tumor sites of the head and neck, but its mode of inactivation does not play a major role in tumor progression. © 2004 Wiley‐Liss, Inc.