Miracle-dz/UniFAR-FTUs huggingface dataset:
Simulated and observed circulation in the Indonesian Seas: 1/12◦ global HYCOM and the INSTANT observations

A 1/12◦ global version of the HYbrid Coordinate Ocean Model (HYCOM) using 3-hourly atmospheric forcing is analyzed and directly compared against observations from the International Nusantara STratification ANd Transport (INSTANT) program that provides the first long-term (2004–2006) comprehensive view of the Indonesian Throughflow (ITF) inflow/outflow and establishes an important benchmark for inter-basin exchange, including the net throughflow transport. The simulated total ITF transport (−13.4 Sv) is similar to the observational estimate (−15.0 Sv) and correctly distributed among the three outflow passages (Lombok Strait, Ombai Strait and Timor Passage). Makassar Strait carries ∼75% of the observed total ITF inflow and while the temporal variability of the simulated transport has high correlation with the observations, the simulated mean volume transport is ∼37% too low. This points to an incorrect partitioning between the western and eastern inflow routes in the model and is the largest shortcoming of this simulation. HYCOM simulates the very deep (>1250 m) overflow at Lifamatola Passage (−2.0 Sv simulated vs. −2.5 Sv observed) ∗ Corresponding author at: NRL Code 7323, Stennis Space Center, MS 39529, USA. Tel. : +1 228 688 4762; fax: +1 228 688 4759. E-mail addresses: joe.metzger@nrlssc.navy. mil (E.J. Metzger), harley.hurlburt@nrlssc.navy. mil (H.E. Hurlburt), xiaobiao.xu@usm.edu (X. Xu), jay.shriver@nrlssc.navy. mil (J.F. Shriver), agordon@ldeo.columbia. edu (A.L. Gordon), jsprintall@ucsd.edu (J. Sprintall), dwi@ldeo.columbia. edu (R.D. Susanto), aken@nioz.nl (H.M. van Aken). 0377-0265/$ – see front matter. Published by Elsevier B.V. doi:10.1016/j.dynatmoce. 2010.04. 002 Author's personal copy 276 E.J. Metzger et al. / Dynamics of Atmospheres and Oceans 50 (2010) 275–300 and indicates overflow contributions originating from the North (South) Equatorial Current in boreal winter–spring (summer–autumn). A new finding of INSTANT is the mean eastward flow from the Indian Ocean toward the interior Indonesian Seas on the north side of Ombai Strait. This flow is not robustly simulated at 1/12◦ resolution, but is found in a 1/25◦ version of global HYCOM using climatological forcing, indicating the importance of horizontal resolution. However, the 1/25◦ model also indicates that the mean eastward flow retroflects, turning back into the main southwestward Ombai Strait outflow, and in the mean does not enter the interior seas to become part of the water mass transformation process. The 1/12◦ global HYCOM is also used to fill in the gaps not measured as part of the INSTANT observational network. It indicates the wide and shallow Java and Arafura Seas carry −0.8 Sv of inflow and that the three major outflow passages capture nearly all the total Pacific to Indian Ocean
The effect of short-term interval training during the competitive season on physical fitness and signs of fatigue: a crossover trial in high-level youth football players.

PURPOSE To analyze performance and fatigue effects of small-sided games (SSG) vs high-intensity interval training (HIIT) performed during a 4-wk in-season period in high-level youth football. METHODS Nineteen players from 4 youth teams (16.5 [SD 0.8] y, 1.79 [0.06] m, 70.7 [5.6] kg) of the 2 highest German divisions completed the study. Teams were randomly assigned to 1 of 2 training sequences (2 endurance sessions per wk): One training group started with SSG, whereas the other group conducted HIIT during the first half of the competitive season. After the winter break, training programs were changed between groups. Before and after the training periods the following tests were completed: the Recovery-Stress Questionnaire for Athletes, creatine kinase and urea concentrations, vertical-jump height (countermovement jump [CMJ], drop jump), straight sprint, agility, and an incremental field test to determine individual anaerobic threshold (IAT). RESULTS Significant time effects were observed for IAT (+1.3%, η(p)(2) = . 31), peak heart rate (-1.8%, η(p)(2) = . 45), and CMJ (-2.3%, η(p)(2) = . 27), with no significant interaction between groups (P > .30). Players with low baseline IAT values (+4.3%) showed greater improvements than those with high initial values (± 0.0%). A significant decrease was found for total recovery (-5.0%, η(p)(2) = . 29), and an increase was found for urea concentration (+9.2%, η(p)(2) = . 44). CONCLUSION Four weeks of in-season endurance training can lead to relevant improvements in endurance capacity. The decreases in CMJ height and total-recovery score together with the increase in urea concentration might be interpreted as early signs of fatigue. Thus, the danger of overtaxing players should be considered.
PAR-2 Deficient CD4+ T Cells Exhibit Downregulation of IL-4 and Upregulation of IFN-γ after Antigen Challenge in Mice.

BACKGROUND To investigate the functional role of protease activated receptor (PAR) -2 in T lymphocytes, we analyzed TCR-mediated inflammatory cytokine production using PAR-2 deficient (KO) and wild type (WT) mice. METHODS Production of serum IgE and cytokines by spleen CD4+ T cells was determined in OVA-sensitized and OVA-challenged mice of PAR-2 KO in contrast to WT mice. Phosphorylation of JNK1 and 2 was determined by Western blotting. RESULTS A reduction in serum levels of IgE and IL-4 production by splenic CD4+ T cells from OVA-sensitized and OVA-challenged KO mice compared to WT mice was observed. By contrast, IFN-γ production was upregulated after antigen stimulation in KO mice. Anti-CD3-mediated phosphorylation of JNK1 was upregulated in splenic CD4+ T cells from KO mice compared to WT mice. CONCLUSIONS PAR-2 participates in the regulation of T cell cytokine production that may be caused by modulation of JNK1 phosphorylation.
Morphological variation among late holocene Mexicans: Implications for discussions about the human occupation of the Americas.

OBJECTIVES Cranial morphology has previously been used to estimate phylogenetic relationships among populations, and has been an important tool in the reconstruction of ancient human dispersals across the planet. In the Americas, previous morphological studies support a scenario of people entering the Americas and dispersing from North America into South America through Meso America, making the Mexican territory the natural funnel through which biological diversity entered South America. MATERIALS AND METHODS We explore the cranial morphological affinities of three late Holocene Mexican series, in relation to ancient and modern crania from North and South America, Australo-Melanesia, and East Asia. Morphological affinities were assessed through Mahalanobis Distances, and represented via Multidimensional Scaling and Ward's Linkage Cluster analysis. Minimum FST values were also calculated for each series. RESULTS Our results show Mexican groups share morphological affinities with the Native American series, but do not cluster together as would be expected. The minimum FST estimates show between-group variation in the Americas is higher than the Asian or Australo-Melanesian populations, and that Mexican series have high between-group variance (FST = 0.124), compared to the geographically larger South America (FST = 0.116) and North America (FST = 0.076). DISCUSSION These results show that the Mexican series share morphological affinities with the East Asian series, but maintains high levels of between-group variation, similar to South America. This supports the suggestion that the high phenotypic variation seen the Americas is not a result of its size, as it can be found in more constricted areas, such as the Mexican territory.
The American Heart Association science advisory on depression and coronary heart disease: An exploration of the issues raised

The American Heart Association issued a science advisory on depression and coronary heart disease (CHD) in 2008. This paper reviews the purpose and content of the advisory and discusses reactions and new information that have followed the advisory’s release. Both the advisory and subsequent data support routine screening for depression in patients with CHD. Such screening can be done efficiently in primary care and cardiology settings and can effectively identify many depressed patients who would otherwise go undetected. Antidepressant drugs such as selective serotonin reuptake inhibitors are safe for use in patients with CHD, can reduce depression, and can improve adherence with medical therapy. Referral to a practice with the knowledge and resources to manage depression promotes successful management of depressed patients with CHD.
A novel mouse Cre‐driver line targeting Perilipin 2‐expressing cells in the neonatal lung

Pulmonary diseases such as chronic obstructive pulmonary disease, lung fibrosis, and bronchopulmonary dysplasia are characterized by the destruction or malformation of the alveolar regions of the lung. The underlying pathomechanisms at play are an area of intense interest since these mechanisms may reveal pathways suitable for interventions to drive reparative processes. Lipid‐laden fibroblasts (lipofibroblasts) express the Perilipin 2 (Plin2) gene‐product, PLIN2, commonly called adipose‐differentiation related protein (ADRP). These cells are also thought to play a role in alveolarization and repair after injury to the alveolus. Progress in defining the functional contribution of lipofibroblasts to alveolar generation and repair is hampered by a lack of in vivo tools. The present study reports the generation of an inducible mouse Cre‐driver line to target cells of the ADRP lineage. Robust Cre‐mediated recombination in this mouse line was detected in mesenchymal cells of the postnatal lung, and in additional organs including the heart, liver, and spleen. The generation and validation of this valuable new tool to genetically target, manipulate, and trace cells of the ADRP lineage is critical for assessing the functional contribution of lipofibroblasts to lung development and repair.
Contacts on GalnAs

The specific contact resistance ρ<inf>c</inf>of Ni/Au-Ge/Ni and Ni/Au-Sn/Ni layers on n-GaInAs and Ni/Au-Mg/Ni and Ni/Au-Zu/Ni on p-GaInAs are measured for different alloying temperatures and times using an extended transmission line model. Specific contact resistances of 4.10<sup>-8</sup>Ω cm<sup>2</sup>for Ni/Au-Sn/Ni on n-GaInAs (n = 10<sup>18</sup>cm<sup>-3</sup>) and 2.10<sup>-5</sup>Ω. cm<sup>2</sup>for Ni/Au-Zn/Ni on p-GaInAs (p = 10<sup>18</sup>cm<sup>-3</sup>) are obtained. After deposition at room temperature, the barrier height of the metal-n-GaInAs system was determined to be 0.16 eV, decreasing below 20 meV after heat treatment. Interdiffusion of metal and semiconductor was investigated by SIMS/Auger measurements. At alloying temperature of 300°C the contacts show fast diffusion of Au relative to the dopants, effecting an increase of the specific contact resistance.
Effects of Canned Cycles and Cutting Parameters on Hole Quality in Cryogenic Drilling of Aluminum 6061-6T

The influence of canned cycles and cutting parameters on hole quality in cryogenic drilling has been investigated experimentally and analytically. A three-level, three-parameter experiment was conducted by using the design-of-experiment methodology. The three levels of independent input parameters were the following: for canned cycles—a chip-breaking canned cycle (G73), a spot drilling canned cycle (G81), and a deep hole canned cycle (G83); for feed rates—0.2, 0.3, and 0.4 mm/rev; and for cutting speeds—60, 75, and 100 m/min. The selected work and tool materials were aluminum 6061-6T and high-speed steel (HSS), respectively. For cryogenic cooling, liquid nitrogen (LN2) was used and was applied externally. The measured output parameters were the three widely used quality characteristics of drilled holes—diameter error, circularity, and surface roughness. Pareto ANOVA was applied for analyzing the results. The findings revealed that the canned cycle has a significant effect on diameter error (contribution ratio 44.09%) and small effects on circularity and surface finish (contribution ratio 7.25% and 6.60%, respectively). The best results for the dimensional accuracy and surface roughness were achieved by G81. G73 produced the best circularity results; however, for dimensional accuracy, it was the worst level. Keywords—Circularity, diameter error, drilling canned cycle, Pareto ANOVA, surface roughness.
The economic burden of spinal muscular atrophy

Abstract Aim: To evaluate the economic burden of spinal muscular atrophy (SMA). Materials and methods: This study used Department of Defense Military Healthcare System (MHS) data from 2003–2012. Healthcare costs were determined for patients with at least one inpatient or three outpatient claims with a diagnosis of SMA before 18 years of age and who had ≥ 6 months of data after first SMA diagnosis or expired within 6 months of initial diagnosis. A comparator cohort was selected using a 3:1 match based on age and gender. Results: A total of 239 individuals with SMA diagnosis met the inclusion criteria along with 717 matched comparator patients. More patients with SMA had hospitalizations (69.5%) compared to the comparator cohort (17.2%, p < 0.001). Median total expenditures across all years of data for patients with SMA were $83 652 (25–75th percentile = $29 620–228 754) vs the comparator group of $4329 (25–75th percentile = $1229–10 062 (p < 0.001)) over an average (SD) of 6.9 ± 3.6 years. The annualized mean costs of total healthcare expenditures were significantly higher for the SMA cases than the comparison cohort, $47 862 ± 88 607 compared to $1861 ± 6374, respectively (p < 0.001). The sub-group of patients with early diagnosis (n = 45) had 4.3 ± 2.9 years of observation with a median cost of $167 921 ($53 349–678 412). Mean age (SD) at first observed SMA diagnosis was 7.5 ± 6.4 years. Mean (SD) duration of follow-up after initial SMA diagnosis was 4.8 ± 3.3 years, with a median post-diagnosis cost of $60 213 ($18 229–192 559). The major costs for all patients were outpatient visits [median = $53 152 ($23 902–136 150)], followed by inpatient costs [median = $11 258 ($0–51 987)] and total prescription costs [median = $3167 ($943–13 283)]. Limitations: The analysis is limited to the data available and may under-estimate the total cost of SMA. Conclusions: Individuals with SMA have a high degree of morbidity, particularly those diagnosed during infancy. SMA patients have significant medical expenditures and high utilization of healthcare services.
RF photonic signal processing components: From high order tunable filters to high stability tunable oscillators

We report on our research and development efforts toward realizing tunable RF photonic filters and tunable local oscillators. In particular, we demonstrate a high order RF photonic filter having 250–1000 MHz bandwidth and more than 70 dBc rejection rate at 2 GHz detuning from the pass-band center. The filter can be tuned across 1–40 GHz frequency range. We also report on our design of a compact tunable RF photonic oscillator with phase noise less than −140 dBc at 100 kHz. The frequency of the oscillator can be tuned from 20 GHz till 35 GHz. We present a theoretical analysis of the capabilities of the devices as well as recent experimental data.
Effects of Leachate from Crumb Rubber and Zinc in Green Roofs on the Survival, Growth, and Resistance Characteristics of Salmonella enterica subsp. enterica Serovar Typhimurium

ABSTRACT The use of green roofs is a growing practice worldwide, particularly in densely populated areas. In an attempt to find new methods for recycling crumb rubber, incorporation of crumb rubber into artificial medium for plant growth in green roofs and similar engineered environments has become an attractive option for the recycling of waste tires. Though this approach decreases waste in landfills, there are concerns about the leaching of zinc and other heavy metals, as well as nutrient and organic compounds, into the environment. The present study analyzed the impact of leachate from crumb rubber and zinc on the growth and viability of Salmonella enterica subsp. enterica serovar Typhimurium. Zinc was chosen for further studies since it has been previously implicated with other biological functions, including biofilm formation, motility, and possible cross-resistance to antimicrobial agents. The study showed that Salmonella can colonize crumb rubber and that crumb rubber extract may provide nutrients that are usable by this bacterium. Salmonella strains with reduced susceptibility (SRS) to zinc were obtained after subculturing in increasing concentrations of zinc. The SRS exhibited differences in gene expression of flux pump genes zntA and znuA compared to that of the parent when exposed to 20 mM added zinc. In biofilm formation studies, the SRS formed less biofilm but was more motile than the parental strain.
A Multi-Criteria Methodology to Support Public Administration Decision Making Concerning Sustainable Energy Action Plans

For municipalities that have joined the Covenant of Mayors promoted by the European Commission, the Sustainable Energy Action Plan (SEAP) represents a strategic tool for achieving the greenhouse gas reductions required by 2020. So far as the energy retrofit actions in their residential building stock are concerned, which in the small-to-medium municipalities are responsible for more than 60% of CO2 emissions, the scenarios for intervening are normally decided on the basis of an economic (cost/performance) analysis. This type of analysis, however, does not take into account important aspects for small and medium-sized communities such as social aspects, environmental impacts, local economic development and employment. A more comprehensive and effective tool to support the choices of public administrators is the multi-criteria analysis. This study proposes a methodology that integrates multi-criteria analysis in order to support Public Administration/Local Authorities in programming Sustainable Energy Action Plans with a more targeted approach to sustainability. The methodology, based on the ELECTRE III method, was applied to a medium-size municipality in the Lombardy region of Italy. The results obtained with this approach are discussed in this paper.
The Fatigue Questionnaire has a good test‐retest profile in IBD

SIRS, I read with interest the validation of the functional assessment of chronic illness therapy‐fatigue (FACIT‐F) in inflammatory bowel disease (IBD) by Tinsley et al. In recent years, there have been an increasing number of papers addressing the problem of fatigue in IBD, which of course is a positive development. However, to be used as measurement tools in clinical trials, questionnaires used to measure fatigue must satisfy basic standards (including validity, reliability, sensitivity, responsiveness and reproducibility). The Fatigue Questionnaire (FQ) was originally developed by Chalder et al. and consists of 11 items that are divided into two main dimensions: physical fatigue (PF) and mental fatigue (MF). In addition to measuring episodic fatigue (irrespective of the duration of symptoms), the FQ contains two questions regarding the duration and extent of fatigue symptoms, which makes it possible to assess the prevalence of chronic fatigue, with a duration of more than 6 months. Recently, we validated the FQ in an IBD population; 5 however, as correctly noted by Tinsley et al., we did not report the test‐retest reliability of the FQ. This may of course cause grounds for speculations about whether the FQ is suitable for longitudinal assessments of fatigue in IBD or not. In Table 1, I therefore present the test‐retest results of the FQ in a subgroup of patients (n = 22) that were deemed to be in a stable condition after 6 months. The intra‐class correlation coefficient reported in Table 1 is the single measure calculated using the two‐way mixed model. The results confirm a high level of agreement between the two occasions, and I can therefore conclude that the FQ is suitable for prospective and longitudinal assessments of fatigue in IBD.
Infection History Determines the Differentiation State of Human CD8+ T Cells

ABSTRACT After the resolution of the acute phase of infection, otherwise quiescent antigen-experienced CD8+ T cells confer rapid protection upon reinfection with viral pathogens or, in the case of persistent viruses, help to maintain control of the infection. Depending on the type of virus, antigen-specific CD8+ T cells have distinct traits, ranging from typical memory cell properties in the case of rapidly cleared viruses to immediate effector functions for persistent viruses. We here show that both the differentiation stage, defined by the expression of cell surface markers, such as CD45RA, CCR7, CD28, and CD27, and distinct expression levels of T-bet and eomesodermin (Eomes) predict the functional profile of antigen-experienced CD8+ T cells. Furthermore, virus-specific CD8+ T cells targeting different respiratory syncytial virus-, influenza A virus-, Epstein-Barr virus (EBV)-, human cytomegalovirus (hCMV)-, and HIV-1-specific epitopes adopt distinct T-bet and Eomes expression patterns that appear to be installed early during the primary response. Importantly, the associations between surface phenotype, T-bet/Eomes expression levels, and the expression of markers that predict CD8+ T-cell function change according to viral infection history, particularly against the background of HIV-1 and, to lesser extent, of human cytomegalovirus and/or Epstein-Barr virus infection. Thus, the functionality of human antigen-experienced CD8+ T cells follows at least two dimensions, one outlined by the surface phenotype and another by the T-bet/Eomes expression levels, which are determined by previous or persistent viral challenges. IMPORTANCE Functional human CD8+ T-cell subsets have been defined using surface markers like CD45RA, CCR7, CD28, and CD27. However, the induction of function-defining traits, like granzyme B expression, is controlled by transcription factors like T-bet and Eomes. Here, we describe how T-bet and Eomes levels distinctly relate to the expression of molecules predictive for CD8+ T-cell function in a surface phenotype-independent manner. Importantly, we found that central memory and effector memory CD8+ T-cell subsets differentially express T-bet, Eomes, and molecules predictive for function according to viral infection history, particularly so in the context of HIV-1 infection and, to lesser extent, of latent EBV- and/or hCMV-infected, otherwise healthy adults. Finally, we show that the distinct phenotypes and T-bet/Eomes levels of different virus-specific CD8+ T-cell populations are imprinted early during the acute phase of primary infection in vivo. These findings broaden our understanding of CD8+ T-cell differentiation.