Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic Signatures of Human Adipose Tissue Hypoxia in Obesity

Adipose tissue (AT) hypoxia has been proposed as the cause of obesity-related AT dysfunction, moving the tissue toward a proinflammatory phenotype. In humans, AT oxygenation has been assessed by expression of hypoxia-sensitive genes or direct assessment of O2 tension; the obvious read out of hypoxia, effects on intermediary metabolism, has not been investigated. We used tissue-specific venous catheterization of subcutaneous abdominal AT in humans to investigate oxygen-related metabolic processes, searching for metabolic signatures relating to hypoxia in obesity. O2 delivery to AT was reduced in obesity (P < 0.05). However, O2 consumption was low (<30% of resting forearm skeletal muscle [SM], P < 0.001); this was not related to obesity. AT primarily oxidized glucose, as demonstrated by a respiratory quotient close to 1.0 (higher than SM, P < 0.05). AT was a net producer of lactate, but there was an inverse relationship in venous outflow between lactate-to-pyruvate ratio (a marker of cytosolic redox state) and BMI, suggesting that AT is glycolytic but obese AT is not hypoxic. Although delivery of O2 to the obese AT is reduced, O2 consumption is low, and metabolic signatures of human AT do not support the notion of a hypoxic state in obesity.
Memory in Patients with Drug‐responsive Mesial Temporal Lobe Epilepsy and Hippocampal Sclerosis

Summary: Purpose: Mesial temporal lobe epilepsy associated with hippocampal sclerosis (MTLE‐HS) is the most common of the antiepileptic drug (AED)‐resistant seizure syndromes that are remediable mostly with surgery, although a small group of patients have benign prognosis with fewer seizures. Material‐specific memory impairment is an important feature in these patients and may be related to both the structural abnormality and the frequent seizures. In this study, we investigated the relation between memory deficit and HS by taking seizure frequency into account.
A STUDY OF TRANSLATION ERROR RATE WITH TARGETED HUMAN ANNOTATION

We define a new, intuitive measure for evaluating machine translation output that avoids the knowledge intensiveness of more meaning-based approaches, and the labor-intensiveness of human judgments. Translation Error Rate (TER) measures the amount of editing that a human would have to perform to change a system output so it exactly matches a reference translation. We also compute a human-targeted TER (or HTER), where the minimum TER of the translation is computed against a human ‘targeted reference’ that preserves the meaning (provided by the reference translations) and is fluent, but is chosen to minimize the TER score for a particular system output. We show that: (1) The single-reference variant of TER correlates as well with human judgments of MT quality as the four-reference variant of BLEU; (2) The human-targeted HTER yields a 33% error-rate reduction and is shown to be very well correlated with human judgments; (3) The four-reference variant of TER and the single-reference variant of HTER yield higher correlations with human judgments than BLEU; (4) HTER yields higher correlations with human judgments than METEOR or its human-targeted variant (HMETEOR); and (5) The four-reference variant of TER correlates as well with a single human judgment as a second human judgment does, while HTER, HBLEU, and HMETEOR correlate significantly better with a human judgment than a second human judgment does.
BMPR1A signaling is necessary for hair follicle cycling and hair shaft differentiation in mice

Interactions between ectodermal and mesenchymal extracellular signaling pathways regulate hair follicle (HF) morphogenesis and hair cycling. Bone morphogenetic proteins (BMPs) are known to be important in hair follicle development by affecting the local cell fate modulation. To study the role of BMP signaling in the HF, we disrupted Bmpr1a, which encodes the BMP receptor type IA (BMPR1A) in an HF cell-specific manner, using the Cre/loxP system. We found that the differentiation of inner root sheath, but not outer root sheath, was severely impaired in mutant mice. The number of HFs was reduced in the dermis and subcutaneous tissue, and cycling epithelial cells were reduced in mutant mice HFs. Our results strongly suggest that BMPR1A signaling is essential for inner root sheath differentiation and is indispensable for HF renewal in adult skin.
Microgeographic Patterns of Genetic Divergence and Adaptation across Environmental Gradients in Boechera stricta (Brassicaceae)*

Abiotic and biotic conditions often vary continuously across the landscape, imposing divergent selection on local populations. We used a provenance trial approach to examine microgeographic variation in local adaptation in Boechera stricta (Brassicaceae), a perennial forb native to the Rocky Mountains. In montane ecosystems, environmental conditions change considerably over short spatial scales, such that neighboring populations can be subject to different selective pressures. Using accessions from southern (Colorado) and northern (Idaho) populations, we characterized spatial variation in genetic similarity via microsatellite markers. We then transplanted genotypes from multiple local populations into common gardens in both regions. Continuous variation in local adaptation emerged for several components of fitness. In Idaho, genotypes from warmer environments (low-elevation or south-facing sites) were poorly adapted to the north-facing garden. In high- and low-elevation Colorado gardens, susceptibility to insect herbivory increased with source elevation. In the high-elevation Colorado garden, germination success peaked for genotypes that evolved at elevations similar to that of the garden and decreased for genotypes from higher and lower elevations. We also found evidence for local maladaptation in survival and fecundity components of fitness in the low-elevation Colorado garden. This approach is a first step in predicting how global change could affect evolutionary dynamics.
Pediatric myelodysplasia: a study of 68 children and a new prognostic scoring system.

Clinical, morphologic, and cytogenetic features were examined in a group of 68 children with myelodysplasia (MDS) referred to a single institution between 1971-1991. The morphologic French-American-British (FAB) system of classification proved of limited value in this group of patients because 50% of the cases were categorized as chronic myelomonocytic leukemia and three patients with eosinophilia and MDS were unclassifiable. Cytogenetic analysis was performed in 63 cases and clonal abnormalities were detected in 55%; the most common chromosome involved was number 7. Modification of the FAB system to incorporate additional diagnostic features such as pretreatment fetal hemoglobin (Hb F) and cytogenetics allowed incorporation of the categories of juvenile chronic myeloid leukemia (JCML) and infantile monosomy 7 syndrome (IMo7). The resulting groups of patients had highly significant differences in survival (P = .00009). The overall 5-year survival for the patients was 31.9% (95% CI 21.7 to 44.1) and factors influencing prognosis included: modified FAB type, platelet count, Hb F level, and cytogenetic complexity. We developed a scoring system ("FPC") where each of the following findings at diagnosis scored one point: HbF greater than 10%, platelets < or = 40 x 10(9)/L, and complex karyotypic changes (two or more clonal structural/numerical abnormalities), which produced groups with highly significant differences, patients with a score of 0 having a 5-year survival of 61.6% (CI 33% to 84%), whereas those with a score of two or three all died within 4 years of diagnosis. The revised classification and scoring system may prove helpful in making treatment choices in pediatric MDS and now needs to be tested prospectively in large scale population-based studies.
A Proteomic Approach for Plasma Biomarker Discovery with iTRAQ Labelling and OFFGEL Fractionation

Human blood plasma contains a plethora of proteins, encompassing not only proteins that have plasma-based functionalities, but also possibly every other form of low concentrated human proteins. As it circulates through the tissues, the plasma picks up proteins that are released from their origin due to physiological events such as tissue remodeling and cell death. Specific disease processes or tumors are often characterized by plasma “signatures,” which may become obvious via changes in the plasma proteome profile, for example, through over expression of proteins. However, the wide dynamic range of proteins present in plasma makes their analysis very challenging, because high-abundance proteins tend to mask those of lower abundance. In the present study, we used a strategy combining iTRAQ as a reagent which improved the peptide ionization and peptide OFFGEL fractionation that has already been shown, in our previous research, to improve the proteome coverage of cellular extracts. Two prefractioning methods were compared: immunodepletion and a bead-based library of combinatorial hexapeptide technology. Our data suggested that both methods were complementary, with regard to the number of identified proteins. iTRAQ labelling, in association with OFFGEL fractionation, allowed more than 300 different proteins to be characterized from 400 μg of plasma proteins.
Unified Scaling of Polar Codes: Error Exponent, Scaling Exponent, Moderate Deviations, and Error Floors

Consider the transmission of a polar code of block length N and rate R over a binary memoryless symmetric channel W and let Pe be the block error probability under successive cancellation decoding. In this paper, we develop new bounds that characterize the relationship of the parameters R, N, Pe, and the quality of the channel W quantified by its capacity I(W) and its Bhattacharyya parameter Z(W). In previous work, two main regimes were studied. In the error exponent regime, the channel W and the rate R <; I(W) are fixed, and it was proved that the error probability Pe scales roughly as 2-√N. In the scaling exponent approach, the channel W and the error probability Pe are fixed and it was proved that the gap to capacity I(W) - R scales as N-1/μ. Here, μ is called scaling exponent and this scaling exponent depends on the channel W. A heuristic computation for the binary erasure channel (BEC) gives μ = 3.627 and it was shown that, for any channel W, 3.579 ≤ μ ≤ 5.702. Our contributions are as follows. First, we provide the tighter upper bound μ <;≤ 4.714 valid for any W. With the same technique, we obtain the upper bound μ ≤ 3.639 for the case of the BEC; this upper bound approaches very closely the heuristically derived value for the scaling exponent of the erasure channel. Second, we develop a trade-off between the gap to capacity I(W)- R and the error probability Pe as the functions of the block length N. In other words, we neither fix the gap to capacity (error exponent regime) nor the error probability (scaling exponent regime), but we do consider a moderate deviations regime in which we study how fast both quantities, as the functions of the block length N, simultaneously go to 0. Third, we prove that polar codes are not affected by error floors. To do so, we fix a polar code of block length N and rate R. Then, we vary the channel W and study the impact of this variation on the error probability. We show that the error probability Pe scales as the Bhattacharyya parameter Z(W) raised to a power that scales roughly like VN. This agrees with the scaling in the error exponent regime.
A fully distributed dual gradient method with linear convergence for large-scale separable convex problems

In this paper we propose a distributed dual gradient algorithm for minimizing linearly constrained separable convex problems and analyze its rate of convergence. In particular, we show that under the assumption that the Hessian of the primal objective function is bounded we have a global error bound type property for the dual problem. Using this error bound property we devise a fully distributed dual gradient scheme for which we derive global linear rate of convergence. The proposed dual gradient method is fully distributed, requiring only local information, since is based on a weighted stepsize. Our method can be applied in many applications, e.g. distributed model predictive control, network utility maximization or optimal power flow.
Individual differences in adult handwritten spelling-to-dictation

We report an investigation of individual differences in handwriting latencies and number of errors in a spelling-to-dictation task. Eighty adult participants wrote a list of 164 spoken words (presented in two sessions). The participants were also evaluated on a vocabulary test (Deltour, 1993). Various multiple regression analyses were performed (on both writing latency and errors). The analysis of the item means showed that the reliable predictors of spelling latencies were acoustic duration, cumulative word frequency, phonology-to-orthographic (PO) consistency, the number of letters in the word and the interaction between cumulative word frequency, PO consistency and imageability. (Error rates were also predicted by frequency, consistency, length and the interaction between cumulative word frequency, PO consistency and imageability.) The analysis of the participant means (and trials) showed that (1) there was both within- and between-session reliability across the sets of items, (2) there was no trade-off between the utilization of lexical and non-lexical information, and (3) participants with high vocabulary knowledge were more accurate (and somewhat faster), and had a differential sensitivity to certain stimulus characteristics, than those with low vocabulary knowledge. We discuss the implications of these findings for theories of orthographic word production.
Feeding Ecology of Dolphinfish in the Western Gulf of Mexico

AbstractDolphinfish Coryphaena hippurus support important commercial and recreational fisheries in the Gulf of Mexico. Understanding the feeding ecology of this economically important pelagic fish is key to its sustainable management; however, dietary data from this region are sparse. We conducted a comprehensive diet study to develop new trophic baselines and investigate potential ontogenetic and sex-related shifts in Dolphinfish feeding ecology. The stomach contents of 357 Dolphinfish (27.6–148.5 cm TL) were visually examined from fishery-dependent sources off Port Aransas, Texas. Our analyses revealed a highly piscivorous diet with Actinopterygii comprising 70.44% of the stomach contents by number. The most commonly observed taxa were carangid (12.45%N) and tetraodontiform (12.08%N; families Balistidae, Monacanthidae, and Tetraodontidae) fishes. Malacostracans were also common (24.83%N), mostly in the form of pelagic megalopae. Other prey categories included squid and the critically endangered Kemp’s R.
Fast Packet Switching for Integrated Services

As the communications industry continues to expand two current trends are becoming apparent: the desire to support an increasing diversity of communications services (voice, video, image, text, etc.) and the consequent requirement for increased network capacity to handle the expected growth in such multi-service tra c. This dissertation describes the design, performance and implementation of a high capacity switch which uses fast packet switching to o er the integrated support of multi-service tra c. Applications for this switch are considered within the public network, in the emerging metropolitan area network and within local area networks. The Cambridge Fast Packet Switch is based upon a non-bu ered, multi-path switch fabric with packet bu ers situated at the input ports of the switch. This results in a very simple implementation suitable for construction in current gate array technology. A simulation study of the throughput at saturation of the switch is rst presented to select the most appropriate switch parameters. Then follows an investigation of the switch performance for multi-service tra c. It is shown, for example, that for an implementation in current CMOS technology, operating at 50 MHz, switches with a total tra c capacity of up to 150 Gbits/sec may be constructed. Furthermore, if the high priority tra c load is limited on each input port to a maximum of 80% of switch port saturation, then a maximum delay across the switch of the order of 100 secs may be guaranteed, for 99% of the high priority tra c, regardless of the lower priority tra c load. An investigation of the implementation of the switch by the construction of the two fundamental components of the design in 3 m HCMOS gate arrays is presented and close agreement is demonstrated between the performance of the hardware implementation and the simulation model. It is concluded that the most likely area of application of this design is as a high capacity multi-service local area network or in the interconnection of such networks.
Acute Type B Aortic Dissection: Does Aortic Arch Involvement Affect Management and Outcomes?: Insights From the International Registry of Acute Aortic Dissection (IRAD)

Background— Stanford Type B acute aortic dissection (TB-AAD) spares the ascending aorta and is optimally managed with medical therapy in the absence of complications. However, the treatment of TB-AAD with aortic arch involvement (AAI) remains an unresolved issue. Methods and Results— We examined 498 patients with TB-AAD enrolled in the International Registry of Acute Aortic Dissection (IRAD) between 1996 and 2003. Kaplan-Meier mortality curves were constructed and multivariate regression models were performed to identify independent predictors of AAI and to evaluate whether AAI was an independent predictor of follow-up mortality. We found that 371 (74.5%) patients with TB-AAD did not have AAI versus 127 (25.5%) with AAI. Independent predictors of AAI were a history of previous aortic surgery (OR 3.4; 95% CI, 1.6 to 7.6; P=0.002), absence of back pain (OR 1.6; 95% CI, 1.1 to 2.5; P=0.05), and any pulse deficit (1.9; 95% CI, 1.1 to 3.3, P=0.03). Mortality for patients without AAI was 9.4%±4.3% and 21.0%±6.9% at 1 and 3 years versus 9.2%±7.7% and 19.9%±11.1% with AAI, respectively (mean follow-up overall, 2.3 years, log rank P=0.82). AAI was not an independent predictor of long-term mortality. Conclusions— Patients with TB-AAD and aortic arch involvement do not differ with regards to mortality at 3 years. Whether or not AAI involvement impacts other measures of morbidity such as freedom from operation or endovascular intervention deserves further study.
Benchmarking File System Benchmarking: It *IS* Rocket Science

The quality of file system benchmarking has not improved in over a decade of intense research spanning hundreds of publications. Researchers repeatedly use a wide range of poorly designed benchmarks, and in most cases, develop their own ad-hoc benchmarks. Our community lacks a definition of what we want to benchmark in a file system. We propose several dimensions of file system benchmarking and review the wide range of tools and techniques in widespread use. We experimentally show that even the simplest of benchmarks can be fragile, producing performance results spanning orders of magnitude. It is our hope that this paper will spur serious debate in our community, leading to action that can improve how we evaluate our file and storage systems.
Conditions modifying development of tumors in mice at various sites by benzo(a)pyrene.

The modifying roles of age, sex, and strain of mice on the incidence, multiplicity, and spectrum of tumors induced by benzo(a)pyrene have been investigated. The first-generation (F1) hybrids of C57BL/6J X C3HeB/FeJ and C3HEB/Fej X A/J mice of both sexes were given single i.p. injections (75 or 150 mug/g) of benzo(a)pyrene at 1, 15, or 42 days of age. Experimental animals were allowed to live their life-spans, while animals in control groups were killed at 52, 90, 142, or 170 weeks of age. Animals treated with benzo(a)pyrene died, in general, by the 100th week of age due to development of liver, lung, stomach and lymphoreticular tumors. Few of the control animals died during that same observational period. The age of mice at the time of exposure to the carcinogen modified development of tumors at all the sites. The sex of animals influenced the development of liver and lymphoreticular tumors. The C3HeB/FeJ X A/J F1 hybrids developed lung tumors more readily than did the C57BL/6J X C3HeB/FeJ F1 mice, which had significantly more liver tumors and neoplasms of the lymphoreticular system than the former strain. No strain difference was observed in regard to tumors at other sites. Higher doses of benzo(a)pyrene were more effective in inducing lung, liver, and stomach tumors. In addition, 5 cases of pancreatic ductal adenoma and adenocarcinoma were observed in carcinogen-treated mice.
Lack of association between fingernail selenium and thyroid cancer risk: a case-control study in French Polynesia.

BACKGROUND Numerous studies have suggested that selenium deficiency may be associated with an increased risk for several types of cancer, but few have focused on thyroid cancer. MATERIALS AND METHODS We examined the association between post-diagnostic fingernail selenium levels and differentiated thyroid cancer risk in a French Polynesian matched case-control study. Conditional logistic regression models were used to estimate odds ratios and 95% confidence intervals. RESULTS The median selenium concentration among controls was 0.76 μg/g. Significantly, we found no association between fingernail selenium levels and thyroid cancer risk after conditioning on year of birth and sex and additionally adjusting for date of birth (highest versus lowest quartile: odds-ratio=1.12, 95% confidence interval: 0.66-1.90; p-trend=0.30). After additional adjustment for other covariates, this association remained non-significant (p-trend=0.60). When restricting the analysis to thyroid cancer of 10 mm or more, selenium in nails was non-significantly positively linked to thyroid cancer risk (p-trend=0.09). Although no significant interaction was evidenced between iodine in nails and selenium in nails effect (p=0.70), a non-significant (p-trend =0.10) positive association between selenium and thyroid cancer risk was seen in patients with less than 3 ppm of iodine in nails. The highest fingernail selenium concentration in French Polynesia was in the Marquises Islands (M=0.87 μg/g) and in the Tuamotu-Gambier Archipelago (M=0.86 μg/g). CONCLUSIONS Our results do not support, among individuals with sufficient levels of selenium, that greater long-term exposure to selenium may reduce thyroid cancer risk. Because these findings are based on post-diagnostic measures, studies with prediagnostic selenium are needed for corroboration.
Better I/O through byte-addressable, persistent memory

Modern computer systems have been built around the assumption that persistent storage is accessed via a slow, block-based interface. However, new byte-addressable, persistent memory technologies such as phase change memory (PCM) offer fast, fine-grained access to persistent storage. In this paper, we present a file system and a hardware architecture that are designed around the properties of persistent, byteaddressable memory. Our file system, BPFS, uses a new technique called short-circuit shadow paging to provide atomic, fine-grained updates to persistent storage. As a result, BPFS provides strong reliability guarantees and offers better performance than traditional file systems, even when both are run on top of byte-addressable, persistent memory. Our hardware architecture enforces atomicity and ordering guarantees required by BPFS while still providing the performance benefits of the L1 and L2 caches. Since these memory technologies are not yet widely available, we evaluate BPFS on DRAM against NTFS on both a RAM disk and a traditional disk. Then, we use microarchitectural simulations to estimate the performance of BPFS on PCM. Despite providing strong safety and consistency guarantees, BPFS on DRAM is typically twice as fast as NTFS on a RAM disk and 4-10 times faster than NTFS on disk. We also show that BPFS on PCM should be significantly faster than a traditional disk-based file system.