Miracle-dz/UniFAR-FTUs huggingface dataset:
The Leucine-responsive Regulatory Protein (Lrp) from Escherichia coli

Lrp (Leucine-responsive regulatory protein) regulates the expression of a number of operons in Escherichia coli. A recent study of DNA sequences recognized by Lrp established the consensus as a 15-bp sequence, YAGHAWATTWTDCTR (Y = C/T, H = “not G,” W = A/T, D =“not C,” R = A/G) (Cui, Y., Wang, Q., Stormo, G. D., and Calvo, J. M. (1995) J. Bacteriol. 177, 4872-4880). Here we report the stoichiometry of Lrp binding (an Lrp dimer binds to a single binding site) and studies that define the minimal length of DNA required for binding. A double-stranded 15 mer having a sequence that closely matches the consensus does not show measurable binding to Lrp. One or two base pairs of DNA flanking each end are not sufficient for binding, but constructs having 3-5 additional base pairs (21 mer) show relatively strong binding. Single-stranded flanking DNA also contributes to strong binding. The extent of the contribution to binding is dependent upon whether the single strand is on the left or right of the double-stranded region and whether the polarity of the single-stranded DNA is 5′ to 3′ or 3′ to 5′.
Automatic Modeling of Urban Facades from Raw LiDAR Point Data

Modeling of urban facades from raw LiDAR point data remains active due to its challenging nature. In this paper, we propose an automatic yet robust 3D modeling approach for urban facades with raw LiDAR point clouds. The key observation is that building facades often exhibit repetitions and regularities. We hereby formulate repetition detection as an energy optimization problem with a global energy function balancing geometric errors, regularity and complexity of facade structures. As a result, repetitive structures are extracted robustly even in the presence of noise and missing data. By registering repetitive structures, missing regions are completed and thus the associated point data of structures are well consolidated. Subsequently, we detect the potential design intents (i.e., geometric constraints) within structures and perform constrained fitting to obtain the precise structure models. Furthermore, we apply structure alignment optimization to enforce position regularities and employ repetitions to infer missing structures. We demonstrate how the quality of raw LiDAR data can be improved by exploiting data redundancy, and discovering high level structural information (regularity and symmetry). We evaluate our modeling method on a variety of raw LiDAR scans to verify its robustness and effectiveness.
Fairness-Constrained Maximum Sum Rate of Multi-Rate CSMA Networks

This paper presents the sum rate analysis of a saturated $M$ -group multi-rate carrier sense multiple access network, where nodes in different groups have distinct packet transmission rates. An explicit expression of the network sum rate is derived, based on which the maximum sum rate is obtained by optimizing the transmission probabilities of nodes. It is found that to achieve the maximum sum rate, only the group of nodes with the largest transmission rate is allowed to access the channel, which leads to severe unfairness. To ensure certain fairness, two constraints, namely, throughput fairness (TF) and data-rate fairness (DF), are proposed, with which each node acquires a target proportion of the network throughput and the network sum rate, respectively. Explicit expressions of the network maximum sum rate with TF and DF are derived, which show that by including the fairness constraints, the network maximum sum rate becomes inferior to that without fairness constraints as long as there is difference in the transmission rates of nodes. The analysis is further applied to IEEE 802.11 networks, where the optimal initial backoff window sizes of nodes to achieve the network maximum sum rates with both fairness constraints are derived.
Thrombopoietin/TGF‐β1 Loop Regulates Megakaryocyte Extracellular Matrix Component Synthesis

Extracellular matrix (ECM) components initiate crucial biochemical and biomechanical cues that are required for bone marrow homeostasis. In our research, we prove that a peri‐cellular matrix composed primarily of type III and type IV collagens, and fibronectin surrounds human megakaryocytes in the bone marrow. The data we collected support the hypothesis that bone marrow megakaryocytes possess a complete mechanism to synthesize the ECM components, and that thrombopoietin is a pivotal regulator of this new function inducing transforming growth factor‐β1 (TGF‐β1) release and consequent activation of the downstream pathways, both in vitro and in vivo. This activation results in a dose dependent increase of ECM component synthesis by megakaryocytes, which is reverted upon incubation with JAK and TGF‐β1 receptor specific inhibitors. These data are pivotal for understanding the central role of megakaryocytes in creating their own regulatory niche within the bone marrow environment. Stem Cells 2016;34:1123–1133
Determinants of real-world functional performance in schizophrenia subjects: correlations with cognition, functional capacity, and symptoms.

OBJECTIVE Impairments in adaptive life skills are a major source of disability in patients with schizophrenia. The relationship between adaptive life skills in real-world settings and performance on neuropsychological tests may be complicated by other factors that interfere with deployment of skills. Assessment of the ability to perform life skills under optimal conditions (i.e., assessment of functional capacity) has been proposed as a means to clarify these relationships. METHOD The authors examined cross-sectional data from a study of the course of neuropsychological and adaptive life skills of older (age 50-85) schizophrenia patients (N=78). Functional capacity was examined with a performance-based measure (UCSD Performance-Based Skills Assessment), and case managers rated real-world adaptive functions (i.e., interpersonal skills, work skills, and community activities). Neuropsychological performance was assessed with a comprehensive battery, while symptoms were assessed with patient self-report and clinical ratings. RESULTS Confirmatory path analyses were used to evaluate the effects of neuropsychological performance, functional capacity, and symptoms on the various domains of real-world functioning. Neuropsychological performance predicted functional capacity, which predicted all three domains of real-world functioning. Depression predicted interpersonal and work skills, while negative symptoms affected interpersonal skills independently of other predictors. CONCLUSIONS Real-world adaptive life skills are predicted by neuropsychological performance, symptoms, and functional capacity. Neuropsychological performance contributes little to the prediction of real-world performance after accounting for functional capacity. In some domains, negative and depressive symptoms influenced real-world performance while not relating to functional capacity or neuropsychological performance.
Narrative Review: The Role of Leptin in Human Physiology: Emerging Clinical Applications

Leptin is a hormone secreted by adipose tissue in direct proportion to amount of body fat. The circulating leptin levels serve as a gauge of energy stores, thereby directing the regulation of energy homeostasis, neuroendocrine function, and metabolism. Persons with congenital deficiency are obese, and treatment with leptin results in dramatic weight loss through decreased food intake and possible increased energy expenditure. However, most obese persons are resistant to the weight-reducing effects of leptin. Recent studies suggest that leptin is physiologically more important as an indicator of energy deficiency, rather than energy excess, and may mediate adaptation by driving increased food intake and directing neuroendocrine function to converse energy, such as inducing hypothalamic hypogonadism to prevent fertilization. Current studies investigate the role of leptin in weight-loss management because persons who have recently lost weight have relative leptin deficiency that may drive them to regain weight. Leptin deficiency is also evident in patients with diet- or exercise-induced hypothalamic amenorrhea and lipoatrophy. Replacement of leptin in physiologic doses restores ovulatory menstruation in women with hypothalamic amenorrhea and improves metabolic dysfunction in patients with lipoatrophy, including lipoatrophy associated with HIV or highly active antiretroviral therapy. The applications of leptin continue to grow and will hopefully soon be used therapeutically.
European stroke prevention study (ESPS): antithrombotic therapy is also effective in the elderly

The ESPS was a multicenter study comparing the effect of the combination of dipyridamole 75 mg and acetylsalicylic acid 330 mg t.i. d. to placebo in 2500 patients (intention‐to‐treat analysis) and 1861 patients (explanatory analysis) in the secondary prevention of stroke or death after one or more attacks of TIA, RIND or stroke of atherothrombotic origin. End‐point reduction was evaluated in two age groups, those not older than 65 years (1358 patients) and those who were older than 65 years (1142 patients). End‐point reduction was significantly greater in patients with active therapy than in the placebo group in both age groups. Subgroup analyses with stroke as an end‐point indicated that younger patients with TIA (≪ 65 years) had lower risk of stroke than those >65 years or patients with stroke. The overall risk reduction was best in TIA patients >65 years of age. The risk reduction with study medication was 40–50% in both sexes and in both age groups. Thus, age of the patient does not influence the efficacy of antithrombotic therapy. However, since these results are obtained from a secondary analysis of a subgroup of patients, the results may need confirmation by further studies.
An economic evaluation of Herceptin in adjuvant setting: the Breast Cancer International Research Group 006 trial.

BACKGROUND Herceptin (trastuzumab) is a humanized monoclonal antibody that is being tested in the adjuvant setting. Cost implications of using trastuzumab, as administered in the Breast Cancer International Research Group 006 trial, are being calculated. This provides information on the treatment's value for money. METHODS Standard breast cancer treatment models were set up for different subpopulations according to stage (I, II, III) and menopausal condition (<50 and >50 years). Costs were calculated from the hospital's point of view, using the micro-costing method. Life expectancy data were based on literature. Our comparator was the existing practice. In addition to a sensitivity analysis, a threshold analysis on the prices of trastuzumab and docetaxel was performed to target an acceptable incremental cost-effectiveness ratio. RESULTS Treatment costs were euro 45,034 (doxorubicin and cyclophosphamide --> docetaxel and trastuzumab) or euro 47,765 (docetaxel, carboplatin and trastuzumab). This was largely (79% and 75%, respectively) attributed to trastuzumab. According to our threshold analysis, an acceptable incremental cost-effectiveness ratio can be reached if health improvements are large enough and/or price discounts are given. CONCLUSIONS Trastuzumab is a promising but very expensive antibody. With the current pressure on health-care budgets, cost implications of using trastuzumab in adjuvant setting must be calculated before use of the product becomes wide-spread. This provides essential information for price-setting policies and for policy makers considering reimbursement.
Male vocalization and female choice in the hybridogenetic Rana lessonae/Rana esculenta complex

In many species, females can improve their fitness by preferring particular males over others. In Palaearctic water frogs of the Rana lessonae/R. esculenta complex the consequences of such mate choice are particularly pronounced. To produce viable offspring, the hybrid R. esculenta (genotype RL) must mate with the parental species R. lessonae (LL); but R. lessonae should avoid mating with R. esculenta, because the resulting hybrid offspring will eliminate the L genome from the germline (hybridogenesis). Hence, there exists a conflict between the sexual parasite (RL) and its sexual host (LL) over the best mating partner. Previous studies have shown a preference for LL males in LL and RL females; but they have also shown that females cannot usually realize their choice when in close proximity to males, because the males forcefully and indiscriminately amplex them. We tested whether females use male vocalizations as a long-distance signal to increase their chances of mating with the preferred LL males. We exposed female R. lessonae and R. esculenta to playbacks of single LL and RL mating calls (experiment 1) and to choruses with a 3:1 excess of LL and RL calls, respectively (experiment 2). In experiment 1, both female types were attracted more by the LL than by the RL calls. In experiment 2, no discrimination between LL- and RL-dominated choruses was observed. The results suggest that females do not use distant male vocalization to approach preferentially ponds or arenas within a pond that hold an excess of LL males. But once they have arrived in a chorus, mating calls from nearby males can direct them to the preferred LL mates. We discuss possible reasons for the failure to discriminate between choruses and the chances for successful choice between individuals within choruses. Copyright 2000 The Association for the Study of Animal Behaviour.
Evaluating the sustainability of the gray-whale-watching industry along the pacific coast of North America

ABSTRACT This paper reports on the first study to critically examine the sustainability of whale-watching practices along the entire migratory range of a pelagic baleen whale species, the gray whale (Eschrichtius robustus). Commercial boat-based whale-watching operations along the west coast of North America were observed for sustainable practices. Data recorded aboard whale-watching vessels and collected via an online survey were integrated into the Lean Six Sigma quality-improvement tool, in order to review business processes and identify where inefficiency or ineffectiveness exists in specific phases within a process. Whale-watching practices were analyzed using this method for 24 whale-watching companies operating in Canada, the United States and Mexico. The results show a high level of variation in management regimes, and operator non-compliance with guidelines, and highlight avenues to eliminate, revise or reduce inefficiency, and improve practices in the interests of high-quality and sustainable operations. We recommend more specific and operational guidelines that allow operators to focus on high compliance with the most critical aspects of their business operation in order to build the sustainability of commercial tourist interactions with gray whales in their migratory range.
Early wound complications of operative treatment of calcaneus fractures: analysis of 190 fractures.

OBJECTIVES The purpose of the present study was to discover any associations between preoperative variables and the occurrence of wound complications in the surgical treatment of calcaneus fractures. DESIGN Retrospective review. SETTING A Level 1 trauma center. PATIENTS One hundred seventy-nine patients, with 190 fractured calcanei, were studied. INTERVENTION Each patient underwent open reduction and internal fixation for calcaneus fractures with standard techniques. MAIN OUTCOME MEASUREMENTS The age, sex, preexisting medical conditions, social history, and mechanism of injury of each patient were recorded. Note was made of the status of the soft tissue injury, if any. The time from injury to surgical stabilization was recorded, as was the type of incision used, use of preoperative antibiotics, and type of wound closure. The patients' records were reviewed for wound complications. These complications were classified as those that could be treated nonsurgically and those that required surgical management. RESULTS Records from July 1992 to July 1998 showed 179 patients who underwent operative stabilization of a calcaneus fracture. Eleven had bilateral fractures, for a total of 190 fractured calcanei. The average age was thirty-five years. Nine patients were diabetics. One hundred eleven of the patients reported current use of cigarettes. Eighteen of the fractures were open. A standard, L-shaped lateral approach to the calcaneus was used in each case. Stabilization was achieved by using standard techniques, with plates and screws. In all cases, a two-layer wound closure was used. Forty-eight patients (25 percent) developed some form of wound complication. Forty (21 percent) of these required surgical treatment. Statistical analysis identified diabetes (p = 0.02; relative risk 3.4), smoking (p = 0.03; relative risk 1.2), and open fractures (p < 0.0001; relative risk 2.8) as risk factors for wound complication. The presence of more than one risk factor increased the relative risk of a wound complication requiring surgery. CONCLUSION Smoking, diabetes, and open fractures all increase the risk of wound complication after surgical stabilization of calcaneus fractures. Cumulative risk factors increase the likelihood of wound complications. Patients who have the risk factors identified in this study should be counseled as to the possible complications that may arise after surgery. In patients with multiple risk factors, consideration should be given to nonsurgical management.
Secondary Particulate Matter in the United States: Insights from the Particulate Matter Supersites Program and Related Studies

Abstract Secondary aerosols comprise a major fraction of fine particulate matter (PM2.5) in all parts of the country, during all seasons, and times of day. The most abundant secondary species include sulfate, nitrate, ammonium, and secondary organic aerosols (SOAs). The relative abundance of each species varies in space and time as a function of meteorology, source emissions strength and type, thermodynamics, and atmospheric processing. Transport of secondary aerosols from upwind locations can contribute significantly at downwind receptor sites, especially regionally in the eastern United States, and across a given urbanized area, such as in Los Angeles. Processes governing the formation of the inorganic secondary species (sul-fate, nitrate, and ammonium) are fairly well understood, although the occurrence of nucleation bursts initiated with the formation of ultrafine sulfuric acid particles observed regionally on clean days in the eastern United States was unexpected. Because of the complex nature of organic material in air, much is still to be learned about the sources, formation, and even spatial and temporal distributions of SOAs. For example, a considerable fraction of ambient organic PM is oxidized organic species, many of which still need to be identified, quantified, and their sources and formation mechanisms determined. Furthermore, significant uncertainty (approaching 50% or more) is associated with estimating the SOA fraction of organic material in air with current methods. This review summarizes the findings of the Supersites Program and related studies addressing secondary particulate matter (PM), including spatial and temporal variations of secondary PM and its precursor species, data and methods for determining the primary and secondary fractions of PM mass, and findings on the anthropogenic and natural fractions of secondary PM.
Phylogenetic Analysis of Clinical Herpes Simplex Virus Type 1 Isolates Identified Three Genetic Groups and Recombinant Viruses

ABSTRACT Herpes simplex virus type 1 (HSV-1) is a ubiquitous human pathogen which establishes lifelong infections. In the present study, we determined the sequence diversity of the complete genes coding for glycoproteins G (gG), I (gI), and E (gE), comprising 2.3% of the HSV-1 genome and located within the unique short (US) region, for 28 clinical HSV-1 isolates inducing oral lesions, genital lesions, or encephalitis. Laboratory strains F and KOS321 were sequenced in parallel. Phylogenetic analysis, including analysis of laboratory strain 17 (GenBank), revealed that the sequences were separated into three genetic groups. The identification of different genogroups facilitated the detection of recombinant viruses by using specific nucleotide substitutions as recombination markers. Seven of the isolates and strain 17 displayed sequences consistent with intergenic recombination, and at least four isolates were intragenic recombinants. The observed frequency of recombination based on an analysis of a short stretch of the US region suggests that most full-length HSV-1 genomes consist of a mosaic of segments from different genetic groups. Polymorphic tandem repeat regions, consisting of two to eight blocks of 21 nucleotides in the gI gene and seven to eight repeats of 3 nucleotides in the gG gene, were also detected. Laboratory strain KOS321 displayed a frameshift mutation in the gI gene with a subsequent alteration of the deduced intracellular portion of the protein. The presence of polymorphic tandem repeat regions and the different genogroup identities can be used for molecular epidemiology studies and for further detection of recombination in the HSV-1 genome.
Joint Transceiver Design for Full-Duplex K-Pair MIMO Interference Channel with Energy Harvesting

In this paper, we propose a joint transceiver design algorithm for the full-duplex (FD) K-pair multiple- input multiple-output (MIMO) interference channel with simultaneous wireless information and power transfer (SWIPT). The aim is to minimize the total transmission power under both transmission rate and energy harvesting (EH) constraints. An iterative algorithm based on alternating optimization and with guaranteed monotonic convergence is proposed to successively optimize the transceiver coefficients. The algorithm consists of three main steps, aimed at successively optimizing: 1) the power splitting (PS) vectors of the EH nodes; 2) the receive beamforming vectors; 3) the transmit beamforming vectors.The first step is carried out based on concave-convex procedure (CCCP), the second step is based on the minimum mean square error (MMSE) criterion and the third step resorts to using semidefinite relaxation (SDR). Simulation results are presented to validate the effectiveness of the proposed algorithm.
A Train-Once Approach for Location Estimation Using the Directional Propagation Model

Location estimation that is based on the mobile phone network has drawn considerable attention in the field of wireless communications. Among the different mobile location estimation methods, the one that estimates a mobile station location with reference to a wave propagation model is shown to be effective and is applicable to different kinds of cellular networks, including Global System for Mobile Communications (GSM), cdmaOne, CDMA2000, and the Universal Mobile Telecommunications System. We have designed a train-once approach for location estimations using the directional propagation model (DPM). The DPM is an improved model that is based on the traditional free-space wave propagation model with the directional gain and environmental factors integrated in the estimation. The train-once approach works because we observe that different types of antennas are designed for different types of environments. Thus, a parameter estimation is related to the antenna type and, in turn, related to the environment. In this paper, we report our study of the train-once approach with the DPM for location estimations. We have tested our model with 192 177 sets of real-life data that have been collected from a major mobile phone operator in Hong Kong. Experimental results show that the train-once approach with the DPM is practical and outperforms the existing location estimation algorithms in terms of accuracy, stability among different types of terrains, and success rates.