Miracle-dz/UniFAR-FTUs huggingface dataset:
A Summary of Landings, Legislative Actions, and Possible Climate-Induced Distribution Shifts in New England Fisheries

New England’s fisheries produce millions of dollars annually, and monitoring and protecting these fisheries ensures the region’s prosperity. There is evidence that the distributional centers of many fish species are shifting north so they remain within their optimal thermal range. Twenty species in New England’s fisheries have been identified as being vulnerable to climate change and, for each of these species, landings data from New England and the Mid-Atlantic were analyzed for the years 1976 – 2015. Trends in landings data were compared to trends in temperature anomaly data. Major legislative events that may have impacted landings data, e.g., fishery closures and reductions in fishing effort, were also examined. The landings data of two out of the 20 species showed clear northward shifts. The remaining 18 species did not display clear trends linking distribution shifts to climate change. Longfin squid (Doryteuthis pealeii) demonstrated a well-defined distributional shift linked to climate change, and is likely to need immediate management action to account for the environmental effects of climate change. Ocean quahog (Arctica islandica), on the other hand, showed a similar landings trend that was not linked to climate change but instead correlated with landing trends in other fisheries. The equivocal nature of most of the results points to the necessity for further study using additional resources like fisheries independent survey data and more precise temperature data. This thesis serves as a background document summarizing the current status of New England fisheries and whether major legislative actions reflect the shifting environmental
Vejle Diabetes Biobank – a resource for studies of the etiologies of diabetes and its comorbidities

Aims Carefully designed and established biobanks are considered one of the most essential resources to foster biomedical research as they provide cost-effective and rapid access to a vast variety of biological materials and related anthropometrics allowing for testing of various biomarkers as well as numerous original and pertinent bioclinical hypotheses related to human disease etiology and prognosis. The objective of the present study was to present the baseline data, design, and methods used for the establishment of the Vejle Diabetes Biobank. Further aims included assessment of the prevalence of diabetes and quality of diabetes treatment in a specified Danish region. Methods The Vejle Diabetes Biobank was established from 2007 to 2010 as a regional Biobank containing blood, DNA, and urine samples from patients with diabetes and a gender- and age-matched control population aged 25–75 years. Anthropometrics were obtained by physical examination, questionnaires, and interviews at the time of inclusion into the Biobank. The cohort was linked to the Danish Civil Registration System, the Danish National Patient Registry, and the Danish National Prescription Registry. Results In total, 4,255 nondiabetic individuals and 3,320 patients with diabetes were included. Type 2 diabetes (T2D) patients had a higher body mass index (30 kg/m2) than type 1 diabetes (T1D) patients (25 and 26 kg/m2 in women and men, respectively) and control subjects (25 and 27 kg/m2 in women and men, respectively). Fasting levels of plasma triglycerides and blood pressure were higher in T2D patients (1.5 mmol/L and 148/85 mmHg, respectively) compared with T1D patients (0.9 mmol/L and 139/81 mmHg, respectively), whereas glycated hemoglobin (HbA1c), plasma high density lipoprotein, low density lipoprotein, and total cholesterol were lower in T2D patients (51 mmol/mol, 1.2 mmol/L, 2.2 mmol/L, and 4.2 mmol/L, respectively) compared with findings in T1D patients (61 mmol/mol, 1.6 mmol/L, 2.3 mmol/L, and 4.4 mmol/L, respectively). At the time of inclusion into the Biobank, 56% of the T2D patients and 25% of T1D patients had an HbA1c <7% (53 mmol/mol). Only 28% and 34% of the T2D patients, respectively, reached treatment target for blood pressure and lipids. Conclusion The Vejle Diabetes Biobank represents one of the largest open diabetes case-control cohorts in Denmark. The Biobank invites collaborative investigations of diabetes and diabetes complication etiologies as well as studies of prognostic or predictive biomarkers.
Defining 3D residue environment in protein structures using SCORPION and FORMIGA

SUMMARY Two web-based applications to analyze amino acids three-dimensional (3D) local environment within protein structures-SCORPION and FORMIGA-are presented. SCORPION and FORMIGA produce a graphical presentation for simple statistical data showing the frequency of residue occurrence within a given sphere (defined here as the 3D contacts). The center of that sphere is placed at the Calpha and at the last heavy atom in the side chain of the selected amino acid. Further depth of detail is given in terms of a secondary structure to which the profiled amino acid belongs. Results obtained with those two applications are relevant for estimating the importance of the amino acid 3D local environment for protein folding and stability. Effectively, SCORPION and FORMIGA construct knowledge-based force fields. The difference between SCORPION and FORMIGA is in that the latter operates on protein interfaces, while the former only functions for a single protein chain. Both applications are implemented as stand-alone components of STING Millennium Suite. AVAILABILITY http://sms.cbi. cnptia.embrapa. br/SMS, http://trantor.bioc. columbia.edu/SMS, http://mirrors.rcsb. org/SMS, http://www.es. embnet.org/SMS and http://www.ar. embnet.org/SMS. [options: Scorpion, Formiga]
Cold-Induced Vasodilation during Single Digit Immersion in 0°C and 8°C Water in Men and Women

The present study compared the thermal responses of the finger to 0 and 8°C water immersion, two commonly used temperatures for cold-induced vasodilation (CIVD) research. On two separate and counterbalanced occasions 15 male and 15 female participants immersed their index finger in 20°C water for 5 min followed by either 0 or 8°C water for 30 min. Skin temperature, cardiovascular and perceptual data were recorded. Secondary analyses were performed between sexes and comparing 0.5, 1 and 4°C CIVD amplitude thresholds. With a 0.5°C threshold, CIVD waves were more prevalent in 8°C (2 (1 – 3) than in 0°C (1.5 (0 – 3)), but the amplitude was lower (4.0 ± 2.3 v 9.2 ± 4.0°C). Mean, minimum and maximum finger temperatures were lower in 0°C during the 30 min immersion, and CIVD onset and peak time occurred later in 0°C. Thermal sensation was lower and pain sensation was higher in 0°C. There were no differences between males and females in any of the physiological or CIVD data with the exception of SBP, which was higher in males. Females reported feeling higher thermal sensations in 8°C and lower pain sensations in 0°C and 8°C compared to males. Fewer CIVD responses were observed when using a 4°C (1 (0 – 3)) threshold to quantify a CIVD wave compared to using a 1°C (2 (0 – 3)) or 0.5°C (2 (0 – 3)) amplitude. In conclusion, both 0 and 8 °C can elicit CIVD but 8°C may be more suitable when looking to optimise the number of CIVD waves while minimising participant discomfort. The CIVD response to water immersion does not appear to be influenced by sex. Researchers should consider the amplitude threshold that was used to determine a CIVD wave when interpreting previous data.
The Molecular Basis of Wound Healing Processes Induced by Lithospermi Radix: A Proteomics and Biochemical Analysis

Lithospermi Radix (LR) is an effective traditional Chinese herb in various types of wound healing; however, its mechanism of action remains unknown. A biochemical and proteomic platform was generated to explore the biological phenomena associated with LR and its active component shikonin. We found that both LR ethanol extracts and shikonin are able to promote cell proliferation by up to 25%. The results of proteomic analysis revealed that twenty-two differentially expressed proteins could be identified when fibroblast cells were treated with LR or shikonin. The functions of those proteins are associated with antioxidant activity, antiapoptosis activity, the regulation of cell mobility, the secretion of collagen, the removal of abnormal proteins, and the promotion of cell proliferation, indicating that the efficacy of LR in wound healing may be derived from a synergistic effect on a number of factors induced by the herbal medicine. Furthermore, an animal model confirmed that LR is able to accelerate wound healing on the flank back of the SD rats. Together these findings help to pinpoint the molecular basis of wound healing process induced by LR.
Increased plasma and renal clearance of an exchangeable pool of apolipoprotein A-I in subjects with low levels of high density lipoprotein cholesterol.

Plasma levels of HDL apo A-I are reduced in individuals with low HDL cholesterol (HDL-C) concentrations as a result of increased fractional catabolic rates (FCRs). To determine the basis for the high apo A-I FCRs, seven subjects with low HDL-C levels (31.0 +/- 4.3 mg/dl) were compared with three subjects with high HDL-C levels (72.0 +/- 4.5 mg/dl). Each subject received autologous HDL that was labeled directly by the iodine-monochloride method (whole-labeled) and autologous HDL that was labeled by exchange with homologous radiolabeled apo A-I (exchange-labeled). Blood was obtained for 2 wk, specific activities determined, and FCRs (d-1 +/- SD) estimated. In every subject, whether in the low or high HDL-C group, the exchange-labeled FCR was greater than the whole-labeled FCR. The exchange-labeled FCR was higher in the low HDL-C group (0.339 +/- 0.043) versus the high HDL-C group (0.234 +/- 0.047; P < 0.009). The whole-labeled FCR was also greater in the low HDL-C group (0.239 +/- 0.023) versus the high HDL-C group (0.161 +/- 0.064; P < 0.02). In addition, in both low and high HDL groups ultracentrifugation resulted in more radioactivity in d > 1.210 (as percentage of total plasma counts per minute) with the exchange-labeled tracer than with the whole-labeled tracer (12.55 +/- 4.95% vs. 1.02 +/- 0.38%; P < 0.003). With both HDL tracers, more radioactivity was found in d > 1.210 in the low versus the high HDL-C groups. When apo A-I catabolism was studied by perfusing isolated rabbit kidneys with whole-labeled HDL, there was twice as much accumulation (cpm/g cortex) of HDL apo A-I isolated from subjects with low HDL-C than from subjects with high HDL-C (P < 0.0025). Finally, HDL that had been isolated from subjects with high levels of HDL-C was triglyceride enriched and exposed to partially purified lipases before perfusion through kidneys. Threefold more apo A-I from modified HDL accumulated in the cortex compared with the unmodified preparation (P < 0.007). The results of these in vivo and ex vivo studies indicate that individuals with low HDL-C levels have more loosely bound, easily exchanged apo A-I and that this exchangeable apo A-I is more readily cleared by the kidney.
Exploring Resilience When Living with a Wound — An Integrative Literature Review

The psychological impact for patients with wounds can be significant, and adverse psychological effects frequently occur when there are permanent changes in the body’s structure or function. Evidence suggests that anxiety, depression and stress can adversely affect the wound healing process. An integrative review examined any paper that discussed any patient in any health care setting who had experienced a psychological impact from the experience of having a wound and the experience of being resilient in that context. Ninety nine papers were located in the initial search with twelve meeting the inclusion criteria and being reviewed. A review of the papers identified that improvement and maintenance of quality of life was perceived to be an important aspect of patient management, but none focused on resilience as a primary endpoint. Further research is required into the clinical benefits of resilient behaviours in patients living with a wound.
Delay-dependent stabilisation of systems with time-delayed state and control: application to a quadruple-tank process

This work presents a study on the stabilisation of linear systems with delays in the control and states, motivated by a benchmark problem from the literature (a quadruple-tank system). A methodology for the stabilisation of this kind of systems is presented, expressing the conditions as LMIs. Using several examples from the literature, it is shown that the proposed stabilisation theorem is less conservative than previous results. Finally, the technique is applied to the benchmark problem, showing how it is possible to derive efficient controllers for realistic problems, using the proposed technique.
The In Utero Programming Effect of Increased Maternal Androgens and a Direct Fetal Intervention on Liver and Metabolic Function in Adult Sheep

Epigenetic changes in response to external stimuli are fast emerging as common underlying causes for the pre-disposition to adult disease. Prenatal androgenization is one such model that results in reproductive and metabolic features that are present in conditions such as polycystic ovary syndrome (PCOS). We examined the effect of prenatal androgens on liver function and metabolism of adult sheep. As non-alcoholic fatty liver disease is increased in PCOS we hypothesized that this, and other important liver pathways including metabolic function, insulin–like growth factor (IGF) and steroid receptivity, would be affected. Pregnant ewes received vehicle control (C; n = 5) or testosterone propionate (TP; n = 9) twice weekly (100 mg; i.m) from d62–102 (gestation 147 days). In a novel treatment paradigm, a second cohort received a direct C (n = 4) or TP (20 mg; n = 7) fetal injection at d62 and d82. In adults, maternal TP exposure resulted in increased insulin secretion to glucose load (P<0.05) and the histological presence of fatty liver (P<0.05) independent of central obesity. Additionally, hepatic androgen receptor (AR; P<0.05), glucocorticoid receptor (GR; P<0.05), UDP- glucose ceramide glucosyltransferase (UGCG; P<0.05) and IGF1 (P<0.01) expression were upregulated. The direct fetal intervention (C and TP) led to early fatty liver changes in all animals without differential changes in insulin secretion. Furthermore, hepatic phosphoenolpyruvate carboxykinase (PEPCK) was up-regulated in the fetal controls (P<0.05) and this was opposed by fetal TP (P<0.05). Hepatic estrogen receptor (ERα; P<0.05) and mitogen activated protein kinase kinase 4 (MAP2K4; P<0.05) were increased following fetal TP exposure. Adult liver metabolism and signaling can be altered by early exposure to sex steroids implicating epigenetic regulation of metabolic disturbances that are common in PCOS.
Exploring the cloud from passive measurements: The Amazon AWS case

This paper presents a characterization of Amazon's Web Services (AWS), the most prominent cloud provider that offers computing, storage, and content delivery platforms. Leveraging passive measurements, we explore the EC2, S3 and CloudFront AWS services to unveil their infrastructure, the pervasiveness of content they host, and their traffic allocation policies. Measurements reveal that most of the content residing on EC2 and S3 is served by one Amazon datacenter, located in Virginia, which appears to be the worst performing one for Italian users. This causes traffic to take long and expensive paths in the network. Since no automatic migration and load-balancing policies are offered by AWS among different locations, content is exposed to the risks of outages. The CloudFront CDN, on the contrary, shows much better performance thanks to the effective cache selection policy that serves 98% of the traffic from the nearest available cache. CloudFront exhibits also dynamic load-balancing policies, in contrast to the static allocation of instances on EC2 and S3. Information presented in this paper will be useful for developers aiming at entrusting AWS to deploy their contents, and for researchers willing to improve cloud design.
Ethnic Differences in Tissue Creatine Kinase Activity: An Observational Study

Background Serum creatine kinase (CK) levels are reported to be around 70% higher in healthy black people, as compared to white people (median value 88 IU/L in white vs 149 IU/L in black people). As serum CK in healthy people is thought to occur from a proportional leak from normal tissues, we hypothesized that the black population subgroup has a generalized higher CK activity in tissues. Methodology/Principal Findings We compared CK activity spectrophotometrically in tissues with high and fluctuating energy demands including cerebrum, cerebellum, heart, renal artery, and skeletal muscle, obtained post-mortem in black and white men. Based on serum values, we conservatively estimated to find a 50% greater CK activity in black people compared with white people, and calculated a need for 10 subjects of one gender in each group to detect this difference. We used mixed linear regression models to assess the possible influence of ethnicity on CK activity in different tissues, with ethnicity as a fixed categorical subject factor, and CK of different tissues clustered within one person as the repeated effect response variable. We collected post-mortem tissue samples from 17 white and 10 black males, mean age 62 y (SE 4). Mean tissue CK activity was 76% higher in tissues from black people (estimated marginal means 107.2 [95% CI, 76.7 to 137.7] mU/mg protein in white, versus 188.6 [148.8 to 228.4] in black people, p = 0.002). Conclusion We found evidence that black people have higher CK activity in all tissues with high and fluctuating energy demands studied. This finding may help explain the higher serum CK levels found in this population subgroup. Furthermore, our data imply that there are differences in CK-dependent ATP buffer capacity in tissue between the black and the white population subgroup, which may become apparent with high energy demands.
The stability of conditional Markov processes and Markov chains in random environments

We consider a discrete time hidden Markov model where the signal is a stationary Markov chain. When conditioned on the observations, the signal is a Markov chain in a random environment under the conditional measure. It is shown that this conditional signal is weakly ergodic when the signal is ergodic and the observations are nondegenerate. This permits a delicate exchange of the intersection and supremum of σ-fields, which is key for the stability of the nonlinear filter and partially resolves a long-standing gap in the proof of a result of Kunita [J. Multivariate Anal. 1 (1971) 365―393]. A similar result is obtained also in the continuous time setting. The proofs are based on an ergodic theorem for Markov chains in random environments in a general state space.
Adipocyte Differentiation-Related Protein Promotes Fatty Acid Storage in Cytosolic Triglycerides and Inhibits Secretion of Very Low–Density Lipoproteins

Objective—We investigated the role of adipocyte differentiation-related protein (ADRP) in triglyceride turnover and in the secretion of very low–density lipoprotein (VLDL) from McA-RH7777 cells and primary rat hepatocytes. Methods and Results—An increase in the expression of ADRP increased triglyceride accumulation in cytosolic lipid droplets and prevented the incorporation of fatty acids into secretable triglycerides, thereby reducing the secretion of triglycerides as well as of apolipoprotein B-100 (apoB-100) and apoB-48 VLDL. The ability of ADRP to block the secretion of apoB-100 VLDL1 decreased with increasing quantities of fatty acids in the medium, indicating a saturable process and emphasizing the importance of sequestering of fatty acids for the effect of ADRP on VLDL secretion. Knockdown (small interfering RNA) of ADRP decreased the pool of cytosolic lipid droplets but increased only the secretion of apoB-48 VLDL1. Additionally, there was an increased flow of fatty acids into &bgr;-oxidation. Conclusions—ADRP is essential for the accumulation of triglycerides in cytosolic lipid droplets. An increase in ADRP prevents the formation of VLDL by diverting fatty acids from the VLDL assembly pathway into cytosolic triglycerides, whereas a decrease of the protein increases the sorting of fatty acids to &bgr;-oxidation and promotes the secretion of apoB-48 VLDL1.
Effect of Inactivation of the Arg- and/or Lys-Gingipain Gene on Selected Virulence and Physiological Properties of Porphyromonas gingivalis

ABSTRACT Proteolytic enzymes produced by Porphyromonas gingivalis are thought to play critical roles in the pathogenesis of periodontitis. The aim of this study was to investigate the effect of gingipain cysteine proteinase gene inactivation on selected pathological and physiological functions of P. gingivalis. Our results showed that Arg- and Lys-gingipain activities are critical components for the efficient growth of P. gingivalis in human serum. However, when the serum was supplemented with peptides provided as pancreatic casein hydrolysate, the gingipains did not appear to be essential for growth. The effect of gingipain gene inactivation on the susceptibility of P. gingivalis to serum bactericidal activity was investigated using standardized human serum. The wild-type strain, P. gingivalis ATCC 33277, was largely unaffected by the bactericidal activity of human serum complement. On the other hand, mutants lacking Arg-gingipain A, Arg-gingipain B, or Lys-gingipain activity were susceptible to complement. Since gingipains are mostly located on the outer membrane of P. gingivalis, inactivation of the genes for these enzymes may modify cell surface properties. We showed that gingipain-deficient mutants differed in their capacities to assimilate radiolabeled amino acids, cause hemolysis, express adhesins, hemagglutinate, and form biofilms. Lastly, the gingipains, more specifically Arg-gingipains, were responsible for causing major cell damage to human gingival fibroblasts. In conclusion, our study indicated that, in addition to being critical in the pathogenic process, gingipains may play a variety of physiological roles in P. gingivalis, including controlling the expression and/or processing of virulence factors. Mutations in gingipain genes thus give rise to pleiotropic effects.
Eye movements of laterally eyed birds are not independent

SUMMARY Most birds have laterally placed eyes with two largely separated visual fields. According to studies in pigeons laterally eyed birds move their eyes independently in most situations, eye coordination just occurred during converging saccades towards frontal stimuli. Here we demonstrate for the first time that laterally eyed zebra finches show coordinated eye movements, regarding direction and amplitude. Spontaneous and visually elicited movements of the two eyes were recorded simultaneously, using a newly developed eye tracking system. We found that, if one eye moves in a certain direction, the other eye simultaneously performs a counter-movement in the opposite direction. Based on these data we developed a hypothesis of how laterally eyed birds cope with the situation in which the left and right eye simultaneously obtain images with different content. We suggest that the counter-movements maintain the spatial relationship of the two visual fields. `Oculospatial constancy', as we call it, facilitates the combination of the left and right visual percept on the level of peripheral or unattended viewing, and the localization of appearing stimuli within the whole visual field. As soon as two visual stimuli simultaneously appear in the left and right visual field, the birds decide on one stimulus and direct the fovea of the appropriate eye towards it for high resolution analysis, the other eye simultaneously performing a counter-saccade. This leads to the assumption that, in contrast to simultaneous peripheral perception with two eyes, the processing of foveal information is possible only for one eye at one time.