Miracle-dz/UniFAR-FTUs huggingface dataset:
A negative regulatory element in the bcl-2 5'-untranslated region inhibits expression from an upstream promoter

bcl-2 mRNA is present at high levels in pre-B-cell lines but is down-regulated in most mature B-cell lines. To investigate the mechanisms responsible for its developmental control, we studied the regulation of bcl-2 expression in human B-lineage cell lines. Using nuclear run-on assays, we found that bcl-2 transcription decreases in parallel with levels of steady-state mRNA during B-cell development. To define cis-acting elements that regulate bcl-2 transcription, we analyzed the expression of transiently transfected promoter-reporter constructs. We identified a novel negative regulatory element (NRE) in the bcl-2 5'-untranslated region that decreased expression from the bcl-2 P1 promoter or heterologous promoters in a position-dependent fashion. The NRE functions in either orientation but contains distinct orientation-dependent subfragments. Additional analyses demonstrated that multiple, functionally redundant sequence elements mediate NRE activity. Though the bcl-2 NRE is active in pre-B- and mature B-cell lines, chromatin structure of the endogenous NRE differs in these cells, suggesting that its activity or effect may vary during B-cell development. Our results indicate that negative control of transcription initiated at the P1 promoter is an important determinant of the differential expression of bcl-2.
Power-Aware CPU Utilization Control for Distributed Real-Time Systems

CPU utilization control has recently been demonstrated to be an effective way of meeting end-to-end deadlines for distributed real-time systems running in unpredictable environments. However, current research on utilization control focuses exclusively on task rate adaptation, which cannot effectively handle rate saturation and discrete task rates. Since the CPU utilization contributed by a real-time periodic task is determined by both its rate and execution time, CPU frequency scaling can be used to adapt task execution times for power-efficient utilization control. In this paper, we present a two-layer coordinated CPU utilization control architecture. The primary control loop uses frequency scaling to locally control the CPU utilization of each processor, while the secondary control loop adopts rate adaptation to control the utilizations of all the processors at the cluster level on a finer timescale. Both the two control loops are designed and coordinated based on well-established control theory for theoretically guaranteed control accuracy and system stability. Empirical results on a physical testbed demonstrate that our control solution outperforms a state-of-the-art utilization control algorithm by having more accurate control and less power consumption.
Positive emotional experiences with portable interactive products

Positive emotions are central to human life and have implications to the overall quality of people's life (Fredrickson, 1998). This paper reports on positive experiences with two types of portable interactive devices (PIDs), specifically media/entertainment and medical/health devices. The study is based on a six-month longitudinal study exploring people's emotional experience and how PIDs mediate these experiences in everyday contexts. Previous findings by the authors (Gomez, Popovic & Blackler, 2011) presented four categories of activities including Feature, Functional, Mediation and Auxiliary activities and their relationship to emotional experience. The paper presents emotional experiences with specific activities reported with a focus on positive emotions. It concludes with a discussion of the findings on positive experiences and the implications for the future design of PIDs.
Reduction in added sugar intake and improvement in insulin secretion in overweight latina adolescents.

BACKGROUND To date, no study has assessed the effects of modifying carbohydrate intake (specifically decreasing added sugar and increasing fiber) on insulin secretion, nor has any study used an overweight Latino adolescent population. The objective of this study was to examine whether changes in dietary intake, specifically reductions in added sugar and/or increases in fiber, following a 12-week, modified carbohydrate dietary intervention, were associated with changes in insulin secretion and other metabolic risk factors for type 2 diabetes. METHODS Participants were 16 overweight (>/=85th percentile BMI) Latina adolescent females (12-17 years) who completed a 12-week modified carbohydrate intervention. Dietary intake was assessed by 3-day diet records, body composition by dual-energy X-ray absorptiometry, and insulin dynamics by an extended 3-hour oral glucose tolerance test (OGTT) at baseline and postintervention. RESULTS There was a trend for unadjusted change in reported added sugar intake (% of kcals) to be associated with change in insulin secretion, i.e. IAUC (r = 0.47; p = 0.075), and this relationship became significant after controlling for age, baseline insulin secretion, added sugar and adiposity, and change in adiposity (r = 0.85; p < 0.05). No other changes in dietary variables were related to changes in insulin secretion or other metabolic risk factors for type 2 diabetes. CONCLUSIONS Participants with greater reductions in added sugar intake showed significantly greater improvements in insulin secretion following a modified carbohydrate nutrition intervention. These findings suggest that interventions focused on decreasing added sugar intake have the potential to reduce type 2 diabetes risk in overweight youth.
Scar formation and lack of regeneration in adult and neonatal liver after stromal injury

Known as a uniquely regenerative tissue, the liver shows a remarkable capacity to heal without scarring after many types of acute injury. In contrast, during chronic liver disease, the liver responds with fibrosis, which can progress to cirrhosis and ultimately liver failure. The cause of this shift from a nonfibrotic to a fibrotic response is unknown. We hypothesized that stromal injury is a key event that prevents restoration of normal liver architecture. To test this, we developed a model of stromal injury using a surgical incision through the normal liver in adult and neonatal mice. This injury produces minimal cell death but locally complete stromal (extracellular matrix) disruption. The adult liver responds with inflammation and stellate cell activation, culminating in fibrosis characterized by collagen deposition. This sequence of events is remarkably similar to the fibrotic response leading to cirrhosis. Studies in neonates reveal a similar fibrotic response to a stromal injury. These findings suggest that extracellular matrix disruption leads not to regeneration but rather to scar, similar to other mammalian organs. These findings may shed light on the pathogenesis of chronic liver disease, and suggest therapeutic strategies.
Chromospheric Cloud-Model Inversion Techniques

Spectral inversion techniques based on the cloud model are extremely useful for the study of properties and dynamics of various chromospheric cloud-like structures. Several inversion techniques are reviewed based on simple (constant source function) and more elaborated cloud models, as well as on grids of synthetic line profiles produced for a wide range of physical parameters by different NLTE codes. Several examples are shown of how such techniques can be used in different chromospheric lines, for the study of structures of the quiet chromosphere, such as mottles/spicules, as well as for active region structures such as fibrils, arch filament systems (AFS), filaments and flares.
Innovative Solutions for Words with Emphasis: Alternative Methods of Braille Transcription

The author of this study proposed two alternative methods for transcribing words with emphasis into braille and compared the use of the symbols for emphasis with the current braille code. The results showed that students were faster at locating words presented in one of the alternate formats, but that there was no difference in students’ accuracy in identifying the indicators and naming the words with emphasis.
TLTF in Cerebrospinal Fluid for Detection and Staging of T. b. gambiense Infection

Background Trypanosome-derived lymphocyte triggering factor (TLTF) is a molecule released by African trypanosomes that interacts with the host immune system, resulting in increased levels of IFN-γ production. Methodology/Principal findings TLTF and anti-TLTF antibodies were assessed in sera and cerebrospinal fluid (CSF) from patients infected with Trypanosoma brucei gambiense (T. b. gambiense) in an attempt to identify alternative markers for diagnosis and stage determination of human African trypanosomiasis or sleeping sickness. Seventy-four serum and sixty-one CSF samples from patients with parasitologically confirmed infection and known disease stage along with 13 sera and CSF from uninfected controls were tested. In serum the levels of anti-TLTF antibodies were unrelated to the disease stage. In contrast, levels of anti-TLTF antibodies in CSF were higher in intermediate/late stages than in early stage disease patients. Specificity of the detected antibodies was assessed by inhibition of TLTF bioactivity as represented by its ability to induce IFN-γ production. Additionally, TLTF was detected in CSF from late stage patients by Western blotting with the anti-TLTF specific monoclonal antibody MO3. Conclusions/Significance These findings suggest a new possibility for disease diagnosis with focus on involvement of the CNS through detection of TLTF and anti-TLTF antibodies in the CSF.
The Role of the S1 State of Carotenoids in Photosynthetic Energy Transfer: The Light-Harvesting Complex II of Purple Bacteria

Using time-dependent density functional theory (TDDFT), we obtained the excitation energy transfer coupling (Coulombic coupling) between the S1 state of rhodopin glucoside (RG) and the Qy state of bacteriochlorophylls (BChl) in the light-harvesting complex II (LH2) of purple photosynthetic bacterium Rhodopseudomonas (Rps.) acidophila. Our results suggest that the small mixing of S2 character arising from symmetry-breaking of the carotenoid plays an important role in the Coulombic coupling. As a result the carotenoid (car) S1 couplings to chlorophylls are similar to a set of scaled down Car(S2)−BChl(Qy) couplings. We also report results for 6,10,15,19-tetramethyl-2-cis-4,6,8,10,12,14,16,18,20-all trans-22-cis-tetracosaundecaene, the polyene backbone of RG with six methyl groups attached, in two different structures: an optimized planar structure and the crystal structure of RG with hydrogen atoms replacing the two end groups, which is distorted from its planar structure. The mixing of S2 configuration is .
Angular Resolved Pathloss Measurements in Urban Macrocell Scenarios at 28 GHz

This paper presents angular resolved measurements in two urban macro scenarios at 28 GHz. The result confirms that the propagation at this relatively high frequency is mainly driven by line-of-sight (LOS) and reflections/scattering. The majority of the energy was contained either in a LOS path or in specular reflections or reflections off smaller objects such as scaffolding, drain pipes, light poles, bikes, and balconies. At all 200 randomly chosen receiver locations up to 350 meters from the transmitter a detectable signal was received in both scenarios and an excess loss of up to 55 dB was measured.
Continuous Monitoring of Distance-Based Range Queries

Given a positive value r, a distance-based range query returns the objects that lie within the distance r of the query location. In this paper, we focus on the distance-based range queries that continuously change their locations in a euclidean space. We present an efficient and effective monitoring technique based on the concept of a safe zone. The safe zone of a query is the area with a property that while the query remains inside it, the results of the query remain unchanged. Hence, the query does not need to be reevaluated unless it leaves the safe zone. Our contributions are as follows: 1) We propose a technique based on powerful pruning rules and a unique access order which efficiently computes the safe zone and minimizes the I/O cost. 2) We theoretically determine and experimentally verify the expected distance a query moves before leaving the safe zone and, for majority of queries, the expected number of guard objects. 3) Our experiments demonstrate that the proposed approach is close to optimal and is an order of magnitude faster than a naïve algorithm. 4) We also extend our technique to monitor the queries in a road network. Our algorithm is up to two order of magnitude faster than a naïve algorithm.
Kit (W-sh) Mice Develop Earlier and More Severe Experimental Autoimmune Encephalomyelitis Due to Absence of Immune Suppression

Mast cells (MCs) have been thought to play a pathogenic role in the development of autoimmune diseases, including experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. However, an immunoregulatory function of these cells has recently been suggested. We investigated the role of MCs in EAE using the W-sh mouse strain, which is MC deficient. W-sh mice developed earlier and more severe clinical and pathological disease with extensive demyelination and inflammation in the CNS. The inflammatory cells were mainly composed of CD4+ T cells, monocyte/macrophages, neutrophils, and dendritic cells. Compared with wild-type mice, MC-deficient mice exhibited an increased level of MCP-1/CCR2 and CD44 expression on CD4+ T cells in addition to decreased production of regulatory T cells, IL-4, IL-5, IL-27, and IL-10. We also found that levels of IL-17, IFN-γ, and GM-CSF were significantly increased in peripheral lymphocytes from immunized W-sh mice compared with those in peripheral lymphocytes from wild-type mice. Reconstitution of W-sh mice downregulated susceptibility to EAE, which correlated with MC recruitment and regulatory T cell activation in the CNS. These findings indicate that responsiveness is not required in the pathogenesis of inflammatory demyelination in the CNS and that, in the absence of MCs, increased MCP-1, CCR2, IL-17, IFN-γ, CD44, and other inflammatory molecules may be responsible for increased severity of EAE.
Effect of Captopril on Pulmonary Artery Pressure Following Corrective Surgery for Tetralogy of Fallot

Abstract Background: This study was designed to investigate the effect of captopril on systolic pulmonary arterial pressure (PAP) and circulating endothelin‐1 (ET‐1) following surgical repair of tetralogy of Fallot (TOF). Methods and Results: Seventy‐six consecutive patients were divided into captopril and control groups following successful repair of TOF. The captopril group was treated with oral captopril (0.2 mg/kg/day) for 12 months. Venous blood was taken before and after the surgery for the analysis of ET‐1. Systolic PAP and ventricular function were assessed by Doppler echocardiography. In the control group, there was an increase in ET‐1 and systolic PAP following the surgery (p < 0.05). In the captopril group, there was no significant increase in the systolic PAP and ET‐1 during the 12‐month follow‐up. The PAP and ET‐1 values in the captopril group were lower than those in the control group following the surgery (p < 0.05). Conclusions: Systolic PAP is elevated following the complete surgical repair of TOF. Increased circulating ET‐1 may be responsible for the elevation of PAP. Captopril treatment prevents postsurgical increases in systolic PAP and circulating ET‐1.
Generating Video Descriptions with Topic Guidance

Generating video descriptions in natural language (a.k.a. video captioning) is a more challenging task than image captioning as the videos are intrinsically more complicated than images in two aspects. First, videos cover a broader range of topics, such as news, music, sports and so on. Second, multiple topics could coexist in the same video. In this paper, we propose a novel caption model, topic-guided model (TGM), to generate topic-oriented descriptions for videos in the wild via exploiting topic information. In addition to predefined topics, i.e., category tags crawled from the web, we also mine topics in a data-driven way based on training captions by an unsupervised topic mining model. We show that data-driven topics reflect a better topic schema than the predefined topics. As for testing video topic prediction, we treat the topic mining model as teacher to train the student, the topic prediction model, by utilizing the full multi-modalities in the video especially the speech modality. We propose a series of caption models to exploit topic guidance, including implicitly using the topics as input features to generate words related to the topic and explicitly modifying the weights in the decoder with topics to function as an ensemble of topic-aware language decoders. Our comprehensive experimental results on the current largest video caption dataset MSR-VTT prove the effectiveness of our topic-guided model, which significantly surpasses the winning performance in the 2016 MSR video to language challenge.
Increased Demand Versus Reduced Supply and the Circadian Variations in Ambulatory Myocardial Ischemia Therapeutic Implications

Although it is now widely accepted that silent myocardial ischemia detected by ambulatory ECG monitoring (AEM) is the most common form of ischemia, the debate regarding the pathophysiological mechanisms responsible for ischemic episodes during daily life is far from being settled.1,2 Because most of the early investigations in this field had reported that the vast majority of transient ischemic episodes (TIEs) occurred during periods of little or no physical activity, it generally was assumed that mechanisms other than an increase in myocardial oxygen demand might be responsible in their genesis.3-5 Although most patients in the earlier investigations had evidence of obstructive lesions secondary to coronary atherosclerosis as well as ischemia secondary to increased oxygen demand during exercise testing, based on relatively lower heart rates during TIEs recorded by AEM, it was suggested that coronary vasoconstriction might play a role in ischemia during daily life.3-6 Little
Construction of optimal resources for concatenated quantum protocols

We present a general framework for the explicit construction of resource states for measurement-based quantum information processing. In particular, we show how to obtain resource states of minimal size for complex tasks that are combinations or concatenations of elementary building blocks. We apply these methods to measurement-based quantum error correction using concatenated quantum error correction codes, code switchers, multiple rounds of entanglement purification, quantum repeaters and combinations thereof.
Plasma membrane calcium ATPase required for semicircular canal formation and otolith growth in the zebrafish inner ear

SUMMARY Fish otoliths consist of >90% calcium carbonate, the accretion of which depends on acellular endolymph. This study confirms the presence of plasma membrane calcium ATPase 1a isoform (Atp2b1a) in the auditory and vestibular system of a teleost fish. As shown by in situ hybridization, zebrafish atp2b1a is expressed mainly in larval otic placode and lateral-line neuromast as well as in the hair cells within the adult zebrafish inner ear chamber. Zebrafish atp2b1a knockdown by antisense morpholinos reduced the number of hair cells and produced malformation of semicircular canals and smaller otoliths. These defects coincide with unbalanced body orientation. The formation of smaller otoliths in atp2b1a morphants may stem from an impairment of calcium supply in the endolymph. However, otolith formation persists in most morphants, suggesting that other zebrafish Atp2b isoforms or paracellular pathways may also transport calcium into the endolymph. These results suggest that Atp2b1a plays an important role for normal development of the auditory and vestibular system as well as calcium transport in the inner ear of zebrafish.
The Costs of Financial Crises: Resource Misallocation, Productivity and Welfare in the 2001 Argentine Crisis

Financial crises in emerging market countries appear to be very costly: output falls are often dramatic, while a host of partial welfare indicators deteriorate as well. The magnitude of the decline in output is puzzling from an accounting perspective, as factor usage does not decline as much as output, resulting in large falls in measured productivity. Furthermore, if productivity is associated with technology, we have no theory to explain why technology should deteriorate during a crisis. In this paper, we present a framework that allows us to account for observed changes in a country's productivity during a financial crises, and to measure the resulting change in the country's welfare. Specifically, we show how to decompose the change in an economy's measured productivity into changes in the efficiency with which resources are allocated across and within sectors and other factors. This framework allows us to measure the welfare costs of a financial crisis, and to decompose these welfare costs into the contributions from changes in technology, in the efficiency of the resource allocation mechanism, in the efficiency of government spending, and in the terms of trade. We apply this framework to the Argentine crisis of 2001 using a combination of national accounts and establishment level data. We find that more than half of the roughly 11% decline in measured total factor productivity can be accounted for by deteriorations in the allocation of resources both across and within sectors. We measure the decline in welfare to be on the order of 15% of one year GDP.
Disease Named Entity Recognition and Normalization using Conditional Random Fields and Levenshtein Distance

This presents a machine learning-based approach for disease named entity recognition and normalization (DNER) subtask of Chemical Disease Relation (CDR) task in BioCreative V. This approach employs a Conditional Random Fields (CRF) based model with domain specific features in biomedical area in disease named entity recognition. In order to improve the performance of entity normalization, the method based on Levenshtein distance is applied. Furthermore, some post-processing techniques were adopted. Experiments on the development set using provided training dataset shows that the proposed approach increases the performance of disease named entity recognition and normalization effectively. In the final evaluation, using the 1,000 PubMed abstracts released as training dataset, this approach achieves F1 performance of 0.7924 on mention level and 0.6050 on the concept level.
Germ‐line transformation of pink bollworm (Lepidoptera: Gelechiidae) mediated by the piggyBac transposable element

The pink bollworm, Pectinophora gossypiella, is a world‐wide pest of cultivated cotton. In certain growing regions populations are suppressed by a sterile release strategy. Efforts to improve the sterile insect technique as well as our understanding of lepidopteran biology could benefit greatly from a germ‐line transformation system. We report transformation of pink bollworm with a piggyBac transposable element carrying the enhanced green flourescent protein (EGFP) marker gene. This vector–marker system resulted in recovery of transgenics at a rate of approximately 3.5%. Integration of the transforming construct that was typical of piggyBac was demonstrated by Southern analysis and sequence determination of transposon flanks. Expression of the EGFP marker was visualized by fluorescent microscopy and Western Blot analysis. Maintenance of transformed strains indicates that the transgene segregates in a Mendelian fashion and has been stable over fourteen generations to date.