Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis

Adaptation to hypoxia is mediated through a coordinated transcriptional response driven largely by hypoxia-inducible factor 1 (HIF-1). We used ChIP-chip and gene expression profiling to identify direct targets of HIF-1 transactivation on a genome-wide scale. Several hundred direct HIF-1 targets were identified and, as expected, were highly enriched for proteins that facilitate metabolic adaptation to hypoxia. Surprisingly, there was also striking enrichment for the family of 2-oxoglutarate dioxygenases, including the jumonji-domain histone demethylases. We demonstrate that these histone demethylases are direct HIF targets, and their up-regulation helps maintain epigenetic homeostasis under hypoxic conditions. These results suggest that the coordinated increase in expression of several oxygen-dependent enzymes by HIF may help compensate for decreased levels of oxygen under conditions of cellular hypoxia.
Thymic Epithelial Cell Development Response to RANKL Promotes Medullary Production in β IRF7-Dependent IFN-

The contributions of IFN regulatory factor (IRF) 3/7 and the type I IFNs IFN- a / b to the innate host defense have been extensively investigated; however, their role in thymic development is less clear. In this study, we show that mice lacking the type I IFN receptor IFN- a / b receptor (IFNAR) or the downstream transcription factor STAT1 harbor a signiﬁcant reduction in self-Ag– presenting, autoimmune regulator (AIRE) + medullary thymic epithelial cells (mTECs). Constitutive IFNAR signaling occurs in the thymic medulla in the absence of infection or inﬂammation. Receptor activator for NF- k B (RANK) ligand stimulation results in IFN- b upregulation, which in turn inhibits RANK signaling and facilitates AIRE expression in mTECs. Finally, we ﬁnd that IRF7 is required for thymic IFN- b induction, maintenance of thymic architecture, and mTEC differentiation. We conclude that spatially and temporally coordinated cross talks between the RANK ligand/RANK and IRF7/IFN- b /IFNAR/STAT1 pathways are essential for differentiation of AIRE + mTECs. The Journal of Immunology , 2013, 190: 000–000.
DEGRADATION THE REFRACTORIES OF ROTARY FURNACE LININGS IN THE PRODUCTION OF ZINC OXIDE

This paper is closely connected with the complex problem of degradation relating to the refractories of rotary furnace linings in the production of zinc oxide. The important factor which has the impact on whole technological process includes choice of the refractory materials. The slag that remains stuck on the walls of furnace linings causes the critical states in the process of production of zinc oxide. The mechanism of degradation of the lining leads to slag rests and it is closely connected with the mutual interaction of the aggressive agents with the components of the lining. Zinc melt with different chemical composition has tendency to be adhered on the surface of the lining. This process creates a new undesired surface layer which increased the overall thickness of slag. Authors recommended a suitable refractory ceramic material for furnace aggregates and they acquired another important knowledge that can be used for modernization and effectiveness relating to the process of industrial production of zinc oxide in practical application.
Waiting to Copy: On the Dynamics of the Market for Technology

We examine the appropriability problem of an inventor who brings to the market a successful innovation that can be legally copied. We study this problem in a dynamic model in which imitators can "enter" the market either by copying the invention at a cost or by buying knowledge (a license) from the inventor. The first imitator to enter the market can then resell his acquired knowledge to the remaining imitators. This dynamic interaction in the licensing market dramatically affects the conventional wisdom on the need for intellectual property rights. Our main result reveals that, in equilibrium, imitators delay their entry into the market and thus the inventor retains monopoly rents for some time. Second, we show that the innovator strictly prefers to offer non-exclusive rather than exclusive licenses which would forbid reselling by the imitators. Last, we prove that when the innovator faces a large number of imitators, her equilibrium reward converges to monopoly profits.
Stevens–Johnson syndrome induced by acetazolamide

Acetazolamide is a sulfonamide derivative and carbonic anhydrase inhibitor used to lower intraocular pressure in glaucomatous patients. Stevens–Johnson syndrome (SJS) toxic epidermal necrolysis (TEN) associated with acetazolamide treatment has been diagnosed in Japanese, Japanese‐American and Indian patients. Herein, we report the second Korean case of SJS‐TEN associated with acetazolamide treatment. The result of human leukocyte antigen (HLA) typing of our patient was positive for HLA‐B59. According to recent research, HLA‐B59 has been detected in SJS caused by metazolamide, which is analogous to acetazolamide. This suggests a possible relationship between genetic background and SJS‐TEN‐associated acetazolamide treatment. Theretofore, acetazolamide should be prescribed to Korean patients with the same discreet caution.
Principal typings for Java-like languages

The contribution of the paper is twofold. First, we define a general notion of type system equipped with an entailment relation between type environments; this generalisation serves as a pattern for instantiating type systems able to support separate compilation and inter-checking of Java-like languages, and allows a formal definition of soundess and completeness of inter-checking w.r. t. global compilation. These properties are important in practice since they allow selective recompilation. In particular, we show that they are guaranteed when the type system has principal typings and provides sound and complete entailment relation between type environments.The second contribution is more specific, and is an instantiation of the notion of type system previously defined for Featherweight Java with method overloading and field hiding. The aim is to show that it is possible to define type systems for Java-like languages, which, in contrast to those used by standard compilers, have principal typings, hence can be used as a basis for selective recompilation.
Affine Invariance Revisited

This paper proposes a Riemannian geometric framework to compute averages and distributions of point configurations so that different configurations up to affine transformations are considered to be the same. The algorithms are fast and proven to be robust both theoretically and empirically. The utility of this framework is shown in a number of affine invariant clustering algorithms on image point data.
Adeno-associated virus serotype 2 induces cell-mediated immune responses directed against multiple epitopes of the capsid protein VP1

Adeno-associated virus serotype 2 (AAV-2) has been developed as a gene therapy vector. Antibody and cell-mediated immune responses to AAV-2 or AAV-2-transfected cells may confound the therapeutic use of such vectors in clinical practice. In one of the most detailed examinations of AAV-2 immunity in humans to date, cell-mediated and humoral immune responses to AAV-2 were characterized from a panel of healthy blood donors. The extent of AAV-2-specific antibody in humans was determined by examination of circulating AAV-2-specific total IgG levels in plasma from 45 normal donors. Forty-one donors were seropositive and responses were dominated by IgG1 and IgG2 subclasses. Conversely, AAV-2-specific IgG3 levels were consistently low in all donors. Cell-mediated immune recall responses were detectable in nearly half the population studied. In vitro restimulation with AAV-2 of peripheral blood mononuclear cell cultures from 16 donors elicited gamma interferon (IFN-γ) (ten donors), interleukin-10 (IL-10) (eight donors) and interleukin-13 (IL-13) (four donors) responses. Using a series of overlapping peptides derived from the sequence of the VP1 viral capsid protein, a total of 59 candidate T-cell epitopes were identified. Human leukocyte antigen characterization of donors revealed that the population studied included diverse haplotypes, but that at least 17 epitopes were recognized by multiple donors and could be regarded as immunodominant. These data indicate that robust immunological memory to AAV-2 is established. The diversity of sequences recognized suggests that attempts to modify the AAV-2 capsid, as a strategy to avoid confounding immunity, will not be feasible.
Failure of physicians to recognize functional disability in ambulatory patients.

OBJECTIVE To assess the ability of internists to identify functional disabilities reported by their patients. DESIGN Comparison of responses by physicians and a random sample of their patients to a 12-item questionnaire about physical and social function. SETTING A hospital-based internal medicine group practice in Boston, Massachusetts, and selected office-based internal medicine practices in Los Angeles, California. SUBJECTS Five staff physicians, three general internal medicine fellows, and 34 internal medicine residents in the hospital-based practice and 178 of their patients. Seventy-six physicians in the office-based practices and 230 of their patients. MEASUREMENTS AND MAIN RESULTS Physicians underestimated or failed to recognize 66% of disabilities reported by patients. Patient-reported disabilities were underestimated or unrecognized more often in the hospital-based practice than in the office-based practices (75% compared with 60%, P less than 0.05). Physicians overstated functional impairment in 21% of paired responses in which patients reported no disability. CONCLUSIONS Physicians often underestimate or fail to recognize functional disabilities that are reported by their patients. They overstate functional impairment to a lesser degree. Because these discrepancies may adversely affect patient care and well-being, medical educators and clinicians should pay more attention to the assessment of patient function.
Implementation of Compressed Sensing in Telecardiology Sensor Networks

Mobile solutions for patient cardiac monitoring are viewed with growing interest, and improvements on current implementations are frequently reported, with wireless, and in particular, wearable devices promising to achieve ubiquity. However, due to unavoidable power consumption limitations, the amount of data acquired, processed, and transmitted needs to be diminished, which is counterproductive, regarding the quality of the information produced. Compressed sensing implementation in wireless sensor networks (WSNs) promises to bring gains not only in power savings to the devices, but also with minor impact in signal quality. Several cardiac signals have a sparse representation in some wavelet transformations. The compressed sensing paradigm states that signals can be recovered from a few projections into another basis, incoherent with the first. This paper evaluates the compressed sensing paradigm impact in a cardiac monitoring WSN, discussing the implications in data reliability, energy management, and the improvements accomplished by in-network processing.
Molecular basis for sterol transport by StART‐like lipid transfer domains

Lipid transport proteins at membrane contact sites, where two organelles are closely apposed, play key roles in trafficking lipids between cellular compartments while distinct membrane compositions for each organelle are maintained. Understanding the mechanisms underlying non‐vesicular lipid trafficking requires characterization of the lipid transporters residing at contact sites. Here, we show that the mammalian proteins in the lipid transfer proteins anchored at a membrane contact site (LAM) family, called GRAMD1a‐c, transfer sterols with similar efficiency as the yeast orthologues, which have known roles in sterol transport. Moreover, we have determined the structure of a lipid transfer domain of the yeast LAM protein Ysp2p, both in its apo‐bound and sterol‐bound forms, at 2.0 Å resolution. It folds into a truncated version of the steroidogenic acute regulatory protein‐related lipid transfer (StART) domain, resembling a lidded cup in overall shape. Ergosterol binds within the cup, with its 3‐hydroxy group interacting with protein indirectly via a water network at the cup bottom. This ligand binding mode likely is conserved for the other LAM proteins and for StART domains transferring sterols.
A Hybrid Approach for Answering Definitional Questions

We present DefScriber, a fully implemented system that combines knowledge-based and statistical methods in forming multi-sentence answers to open-ended deﬁnitional questions of the form, “What is X? ” We show how a set of deﬁnitional predicates proposed as the knowledge-based side of our approach can be used to guide the selection of deﬁnitional sentences. Finally, we present results of an evaluation of deﬁnitions generated by DefScriber from Internet documents.
Modifiable arousal in ADHD and its etiological association with fluctuating reaction times

BACKGROUND: Cognitive theories of attention-deficit/hyperactivity disorder (ADHD) propose that high within-subject fluctuations of cognitive performance in ADHD, particularly reaction time (RT) variability (RTV), may reflect arousal dysregulation. Yet, direct evidence of arousal dysregulation and how it may account for fluctuating reaction times in ADHD is limited. We used skin conductance (SC) as a measure of peripheral arousal and aimed to investigate its phenotypic and familial association with RTV in a large sample of ADHD and control sibling pairs. METHODS: 292 adolescents and young adults, consisting of 73 participants with ADHD and their 75 siblings, as well as 72 controls and their 72 siblings, completed the baseline (slow, unrewarded) and fast-incentive conditions of a RT task, whilst SC was simultaneously recorded. RESULTS: A significant group by condition interaction emerged for SC level (SCL). Participants with ADHD had decreased SCL, compared to controls, in the baseline but not fast-incentive condition. Baseline SCL was negatively associated with RTV and multivariate model fitting demonstrated that the covariance of SCL with RTV, and of SCL with ADHD, was mostly explained by shared familial effects. CPNCLUSIONS: ADHD is associated with decreased, but modifiable, tonic peripheral arousal. A shared familial etiology underlies the relationship between arousal and RTV, and between arousal and ADHD. Given the malleability of SCL, if our findings are replicated, it warrants further exploration as a potential treatment target for ADHD.
OLM: Opportunistic Layered Multicasting for Scalable IPTV over Mobile WiMAX

We propose Opportunistic Layered Multicasting (OLM), a joint user scheduling and resource allocation algorithm that provides enhanced quality and efficiency for layered video multicast over Mobile WiMAX. This work is a lead off and complete synergy of layered video multicasting with opportunistic concept. The target application is characterized by groups of users acquiring popular video programs over a fading channel. To accommodate various bandwidth requirements and device capability, video streams are coded into base and enhancement layers using scalable video coding technology. Correspondingly, the optimization problems, which select the best subset of users to receive a specific video layer and assign the most appropriate modulation and coding scheme for this video layer, are specifically formulated for both video layer types. We also design fast and effective algorithms to bridge the gap between theoretical throughput capacity and implementation concerns. Thus, the basic video quality can be efficiently guaranteed to all subscribers while creating most utility out of limited resources on enhancement information. To overcome the inevitable packet loss in a multicast session, an FEC rate adaptation scheme to approach theoretical performance is also presented. Favorable performance of the proposed algorithms is demonstrated by simulations utilizing realistic Mobile WiMAX parameters.
Correlation-preserved non-Gaussian statistical timing analysis with quadratic timing model

Recent study shows that the existing first order canonical timing model is not sufficient to represent the dependency of the gate delay on the variation sources when processing and operational variations become more and more significant. Due to the nonlinearity of the mapping from variation sources to the gate/wire delay, the distribution of the delay is no longer Gaussian even if the variation sources are normally distributed. A novel quadratic timing model is proposed to capture the non-linearity of the dependency of gate/wire delays and arrival times on the variation sources. Systematic methodology is also developed to evaluate the correlation and distribution of the quadratic timing model. Based on these, a novel statistical timing analysis algorithm is propose which retains the complete correlation information during timing analysis and has the same computation complexity as the algorithm based on the canonical timing model. Tested on the ISCAS circuits, the proposed algorithm shows 10 /spl times/ accuracy improvement over the existing first order algorithm while no significant extra runtime is needed.
Robust transmission of multimedia data over power-lines

In this paper, we jointly consider the source and channel coding problem with transmission over power line channels. We propose frame based multiple description (MD) video coding with an efficient reconstruction algorithm. Further, transmission deploys wide-band impulse modulation with bit interleaved convolutional channel coding. The MD video coder uses a redundant filterbank to generate multiple descriptions of the original video stream, and allows for exact signal reconstruction even in the presence of packet losses. In the presence of packet losses, we adopt a "restoring stage" before the synthesis filterbank whose purpose is to recover the lost coefficients. This solution has limited computational complexity and does not introduce excessive delay in interactive applications. We compare the robustness of the proposed solution with that of another MD solution based on polyphase spatial subsampling assuming wideband impulsive transmission over a power-line link with rate of 1.6 Mbps.
Estimating change in cardiovascular disease and diabetes burdens due to dietary and metabolic factors in Korea 1998–2011: a comparative risk assessment analysis

Objectives Over the past 10 years, the burden of chronic diseases in Korea has increased. However, there are currently no quantitative estimates of how changes in diet and metabolic factors have contributed to these shifting burdens. This study aims to evaluate the contributions of dietary and metabolic risk factors to death from cardiometabolic diseases (CMDs) such as cardiovascular conditions, strokes and diabetes in Korea, and to estimate how these contributions have changed over the past 10 years (1998–2011). Design and methods We used data on 6 dietary and 4 metabolic risk factors by sex, age and year from the Korea National Health and Nutrition Examination Survey. The relative risks for the effects of the risk factors on CMD mortality were obtained from meta-analyses. The population-attributable fraction attributable to the risk factors was calculated by using a comparative risk assessment approach across sex and age strata (males and females, age groups 25–34, 35–44, 45–54, 55–64, 65–74 and 75+ years) from 1998 to 2011. Results The results showed that a suboptimal diet and high blood pressure were the main risk factors for CMD mortality in Korea. High blood pressure accounted for 127 096 (95% uncertainty interval (UI): 121 907 to 132 218) deaths from CMD. Among the individual dietary risk factors, a high intake of sodium (42 387 deaths; 95% UI: 42 387 to 65 094) and a low intake of fruit (50 244 deaths; 95% UI: 40 981 to 59 178) and whole grains (54 248 deaths; 95% UI: 47 020 to 61 343) were responsible for the highest number of CMD deaths in Korea. Conclusions Indicating the relative importance of risk factors in Korea, the results suggest that metabolic and dietary risk factors were major contributors to CMD mortality.
Technique and Apparatus for Accurate Cross-Sectional Stress Profiling of Optical Fibers

The design and performance of a technique for determining 2-D cross-sectional stress distributions in optical fibers and fiber-based devices is described. The Brace-Köhler phase compensation method is implemented on a commercial polarization microscope to perform full-field measurements of the transverse retardations induced by the low levels of birefringence in optical fibers. Analysis of the region surrounding the fiber enables removal of the background retardation induced by the imaging optics. A custom microscope stage plate, fiber rotation apparatus, and compensator rotation apparatus allow for semi-automated measurements at various angular orientations of the fiber. Image analysis techniques are described that reduce the number of angular increments over which the compensator must be rotated, thus providing a more workable total data acquisition time. Computed tomography principles and the filtered backprojection algorithm are implemented to determine full cross-sectional axial stress distributions. The lateral spatial resolution of the technique is 0.46 μm . The axial stress distribution in Corning SMF-28 fiber is presented. The resolution of the axial stress determined with the technique is estimated to be 0.24 MPa. The accuracy of the axial stress is estimated to be ±0.18 MPa.
Encoding High Dimensional Local Features by Sparse Coding Based Fisher Vectors

Deriving from the gradient vector of a generative model of local features, Fisher vector coding (FVC) has been identified as an effective coding method for image classification. Most, if not all, FVC implementations employ the Gaussian mixture model (GMM) to characterize the generation process of local features. This choice has shown to be sufficient for traditional low dimensional local features, e.g., SIFT; and typically, good performance can be achieved with only a few hundred Gaussian distributions. However, the same number of Gaussians is insufficient to model the feature space spanned by higher dimensional local features, which have become popular recently. In order to improve the modeling capacity for high dimensional features, it turns out to be inefficient and computationally impractical to simply increase the number of Gaussians. In this paper, we propose a model in which each local feature is drawn from a Gaussian distribution whose mean vector is sampled from a subspace. With certain approximation, this model can be converted to a sparse coding procedure and the learning/inference problems can be readily solved by standard sparse coding methods. By calculating the gradient vector of the proposed model, we derive a new fisher vector encoding strategy, termed Sparse Coding based Fisher Vector Coding (SCFVC). Moreover, we adopt the recently developed Deep Convolutional Neural Network (CNN) descriptor as a high dimensional local feature and implement image classification with the proposed SCFVC. Our experimental evaluations demonstrate that our method not only significantly outperforms the traditional GMM based Fisher vector encoding but also achieves the state-of-the-art performance in generic object recognition, indoor scene, and fine-grained image classification problems.