Miracle-dz/UniFAR-FTUs huggingface dataset:
Relationships between heart rate target determined in different exercise testing in COPD patients to prescribed with individualized exercise training

Background It has been scientifically proven that pulmonary rehabilitation improves exercise tolerance and facilitates the carrying out of daily physical activities. To optimize the physical and physiological benefits, it is necessary to individualize the training intensity for each patient. The aim of this study is to compare the heart rate (HR) responses to three exercise modalities measuring aerobic fitness in chronic obstructive pulmonary disease patients, in order to easily prescribe individual target HRs for endurance training. Patients and method Fifty COPD patients (mean age: 60.1±8.5 years) were included in the study. Each patient carried out a cardiopulmonary exercise test, a 6-minute walk test (6MWT) and a 6-minute stepper test (6MST). During these tests, HR was recorded continuously. After the cardiopulmonary exercise test, the HR was noted at the ventilatory threshold (VT) and at the end of the two exercise field tests (6MWTpeak and 6MSTpeak). The values of the HR during the last 3 minutes of both field tests were averaged (6MWT456 and 6MST456). Finally, the HR at 60% of the HR reserve was calculated with the values of the HR measured during 6MWT and 6MST (HRr60%walk, HRr60%step). Results The HRs measured during the 6MST were significantly higher than those measured during the 6MWT. The HRr60%step was not significantly different from 6MWT456 and 6MWTpeak HR (P=0.51; P=0.48). A significant correlation was observed between 6MWT456 and 6MWTpeak (r=0.58). The 6MWT456 and 6MWTpeak HR were correlated with HRr60%step (r=0.68 and r=0.62). The VT could be determined in 28 patients. The HRVT was not different from 6MWT456, 6MWTpeak, and HRr60%step (P=0.57, P=0.41 and P=0.88) and was correlated to 6MWT456, 6MWTpeak, and HRr60%step (r=0.45, r=0.40, r=0.48). Conclusion An individualized target HR for endurance training can be prescribed from the HR measured during routine tests, such as 6MWT or 6MST.
Natural Blood Feeding and Temperature Shift Modulate the Global Transcriptional Profile of Rickettsia rickettsii Infecting Its Tick Vector

Rickettsia rickettsii is an obligate intracellular tick-borne bacterium that causes Rocky Mountain Spotted Fever (RMSF), the most lethal spotted fever rickettsiosis. When an infected starving tick begins blood feeding from a vertebrate host, R. rickettsii is exposed to a temperature elevation and to components in the blood meal. These two environmental stimuli have been previously associated with the reactivation of rickettsial virulence in ticks, but the factors responsible for this phenotype conversion have not been completely elucidated. Using customized oligonucleotide microarrays and high-throughput microfluidic qRT-PCR, we analyzed the effects of a 10°C temperature elevation and of a blood meal on the transcriptional profile of R. rickettsii infecting the tick Amblyomma aureolatum. This is the first study of the transcriptome of a bacterium in the genus Rickettsia infecting a natural tick vector. Although both stimuli significantly increased bacterial load, blood feeding had a greater effect, modulating five-fold more genes than the temperature upshift. Certain components of the Type IV Secretion System (T4SS) were up-regulated by blood feeding. This suggests that this important bacterial transport system may be utilized to secrete effectors during the tick vector’s blood meal. Blood feeding also up-regulated the expression of antioxidant enzymes, which might correspond to an attempt by R. rickettsii to protect itself against the deleterious effects of free radicals produced by fed ticks. The modulated genes identified in this study, including those encoding hypothetical proteins, require further functional analysis and may have potential as future targets for vaccine development.
Shadow Detection and Geo-tagged Image Information Based Strategic Infrastructure Characterization

Exploring the significance of geo-tagged information of a satellite image and associated shadow information in the image to enable man-made infrastructure dimensional characterization, in this paper a novel approach has been developed to estimate the height of a man-made structure accurately. Our proposed method applies shadow detection and shadow feature along with geo-tagged information retrieved through Google Earth tools, to estimate the structural dimension of the man-made infrastructure. To characterize the dimensional features of the man-made structure, we have considered Google Earth satellite images with precise and crisp edge as well as shadow length information, which have been obtained using freely available Google Earth information retrieval tool. Applying our proposed mathematical formulation, the height of man-made structures as well as neighbouring structures have been estimated which can be used for certain strategic decision purposes. The proposed method can be applicable for professionals exploring dimensional characterization of relatively low height constructions as well as defence purposes. Our proposed model has outperformed majority of existing approaches, particularly in terms of accuracy of height estimation of man-made structures.
A population‐based approach to analyzing pulses in time series of hormone data

Studies of reproductive physiology involve rapid sampling protocols that result in time series of hormone concentrations. The signature pattern in these times series is pulses of hormone release. Various statistical models for quantifying the pulsatile release features exist. Currently these models are fitted separately to each individual and the resulting estimates averaged to arrive at post hoc population‐level estimates. When the signal‐to‐noise ratio is small or the time of observation is short (e.g., 6 h), this two‐stage estimation approach can fail. This work extends the single‐subject modelling framework to a population framework similar to what exists for complex pharamacokinetics data. The goal is to leverage information across subjects to more clearly identify pulse locations and improve estimation of other model parameters. This modelling extension has proven difficult because the pulse number and locations are unknown. Here, we show that simultaneously modelling a group of subjects is computationally feasible in a Bayesian framework using a birth–death Markov chain Monte Carlo estimation algorithm. Via simulation, we show that this population‐based approach reduces the false positive and negative pulse detection rates and results in less biased estimates of population‐level parameters of frequency, pulse size, and hormone elimination. We then apply the approach to a reproductive study in healthy women where approximately one‐third of the 21 subjects in the study did not have appropriate fits using the single‐subject fitting approach. Using the population model produced more precise, biologically plausible estimates of all model parameters. Copyright © 2017 John Wiley & Sons, Ltd.
A new brain dopamine‐deficient Drosophila and its pharmacological and genetic rescue

Dopamine (DA) is a neurotransmitter with conserved behavioral roles between invertebrate and vertebrate animals. In addition to its neural functions, in insects DA is a critical substrate for cuticle pigmentation and hardening. Drosophila tyrosine hydroxylase (DTH) is the rate limiting enzyme for DA biosynthesis. Viable brain DA‐deficient flies were previously generated using tissue‐selective GAL4‐UAS binary expression rescue of a DTH null mutation and these flies show specific behavioral impairments. To circumvent the limitations of rescue via binary expression, here we achieve rescue utilizing genomically integrated mutant DTH. As expected, our DA‐deficient flies have no detectable DTH or DA in the brain, and show reduced locomotor activity. This deficit can be rescued by l‐DOPA/carbidopa feeding, similar to human Parkinson's disease treatment. Genetic rescue via GAL4/UAS‐DTH was also successful, although this required the generation of a new UAS‐DTH1 transgene devoid of most untranslated regions, as existing UAS‐DTH transgenes express in the brain without a Gal4 driver via endogenous regulatory elements. A surprising finding of our newly constructed UAS‐DTH1m is that it expresses DTH at an undetectable level when regulated by dopaminergic GAL4 drivers even when fully rescuing DA, indicating that DTH immunostaining is not necessarily a valid marker for DA expression. This finding necessitated optimizing DA immunohistochemistry, showing details of DA innervation to the mushroom body and the central complex. When DA rescue is limited to specific DA neurons, DA does not diffuse beyond the DTH‐expressing terminals, such that DA signaling can be limited to very specific brain regions.
The Health related Quality of Life of Puerto Ricans during Cancer Treatments; A Pilot Study.

OBJECTIVE To examine the health related quality of life (HRQOL) experienced by 79 Puerto Rican adults during cancer treatments. METHODS This study used a descriptive, cross-sectional design. Participants completed a demographics form and the Functional Assessment of Cancer Therapy-General QOL questionnaire (FACT-G). Descriptive statistics were generated. RESULTS Participants were ages 28-78; most of the participants had breast (38.0%), prostate (14.0%) and cervical and ovarian cancers (10.1%) treated with chemotherapy (45.6%). The participants had a mean total score on the FACT-G of 75.2 (SD = 18.9). As a group, the functional well-being was the most affected (mean 17.2, SD 6.8), and the Social/Familial was the least affected (mean 20.7, SD 6.0). CONCLUSION Cancer is the leading cause of death in the island of Puerto Rico. Female Puerto Rican cancer patients in this study sample had increased risk for experiencing worse: overall HRQOL, physical well-being and emotional well-being compared to males. Given that the Hispanic oncology population does not always report symptoms, risking under-assessment and under management, this suggests there may be a greater need for HRQOL surveillance for this population.
Analysis of expression of cyclin E, p27kip1 and Ki67 protein in colorectal cancer tissues and its value for diagnosis, treatment and prognosis of disease.

OBJECTIVE We conducted this study is to investigate the clinical application value of Cyclin E, p27kip1 and Ki67 protein expression in colorectal cancer tissues for diagnosis, treatment, and prognosis of this disease. PATIENTS AND METHODS The positive expression of Cyclin E, p27kip1 and Ki-67 in tissues of 200 patients with colorectal cancer and 200 patients with benign colorectal tumor or inflammation were detected by immunohistochemistry PowerVision two-step method. RT-PCR was used to detect the expression level of the corresponding mRNA, as well as to analyze the association with TNM staging, pathology type, free progression survival and median survival. The sensitivity, specificity, and accuracy of diagnosis were analyzed by ROC. RESULTS The positive expression rate and positive degree of Cyclin E and Ki-67 of observation group were higher than those of the control group, while positive expression rate and positive degree of p27kipl was lower than that of the control group; the differences were statistically significant (p<0.05). The quantitative expression levels of Cyclin E and Ki-67 mRNA of observation group were distinctly higher than those of the control group, while p27kipl was evidently lower than that of the control group; the differences were statistically significant (p<0.05). With the increase of TNM staging, the positive expression of Cyclin E and Ki-67 increased, p27kipl decreased, and the difference was statistically significant (p<0.05). With the decrease of differentiation degree, the positive expression of Cyclin E and Ki-67 increased, p27kipl decreased, and the difference was statistically significant (p<0.05). The free progression survival and median survival of positive expression and negative expression of Cyclin E and Ki-67 were shortened, p27kipl extended, and the difference was statistically significant (p<0.05). The diagnostic sensitivity of Cyclin E mRNA was 89.6%, specificity 84.5%, accuracy 0.823 and the critical value was 0.3562; The diagnostic sensitivity of p27kipl mRNA was 80.5%, specificity 76.5%, accuracy 0.802 and the critical value was 0.3023. The diagnostic sensitivity of Ki-67 mRNA was 86.5%, specificity 82.9%, accuracy 0.814 and the critical value was 0.3243. CONCLUSIONS We discovered that Cyclin E and Ki67 protein expression of colorectal cancer tissues was upregulated and p27kipl protein expression was downregulated, which were closely related to the TNM and pathological differentiation degree. These values were also closely associated with free progression survival and median survival of prognosis. Therefore, the above indexes can be used as highly sensitive, specific and accurate markers for the diagnosis of colorectal cancer.
Testing the Stress-Gradient Hypothesis at the Roof of the World: Effects of the Cushion Plant Thylacospermum caespitosum on Species Assemblages

Many cushion plants ameliorate the harsh environment they inhabit in alpine ecosystems and act as nurse plants, with significantly more species growing within their canopy than outside. These facilitative interactions seem to increase with the abiotic stress, thus supporting the stress-gradient hypothesis. We tested this prediction by exploring the association pattern of vascular plants with the dominant cushion plant Thylacospermum caespitosum (Caryophyllaceae) in the arid Trans-Himalaya, where vascular plants occur at one of the highest worldwide elevational limits. We compared plant composition between 1112 pair-plots placed both inside cushions and in surrounding open areas, in communities from cold steppes to subnival zones along two elevational gradients (East Karakoram: 4850–5250 m and Little Tibet: 5350–5850 m). We used PERMANOVA to assess differences in species composition, Friedman-based permutation tests to determine individual species habitat preferences, species-area curves to assess whether interactions are size-dependent and competitive intensity and importance indices to evaluate plant-plant interactions. No indications for net facilitation were found along the elevation gradients. The open areas were not only richer in species, but not a single species preferred to grow exclusively inside cushions, while 39–60% of 56 species detected had a significant preference for the habitat outside cushions. Across the entire elevation range of T. caespitosum, the number and abundance of species were greater outside cushions, suggesting that competitive rather than facilitative interactions prevail. This was supported by lower soil nutrient contents inside cushions, indicating a resource preemption, and little thermal amelioration at the extreme end of the elevational gradient. We attribute the negative associations to competition for limited resources, a strong environmental filter in arid high-mountain environment selecting the stress-tolerant species that do not rely on help from other plants during their life cycle and to the fact the cushions do not provide a better microhabitat to grow in.
Development and Validation of the Physics Anxiety Rating Scale.

This study reports the development and validation process for an instrument to measure university students’ anxiety in physics courses. The development of the Physics Anxiety Rating Scale (PARS) included the following steps: Generation of scale items, content validation, construct validation, and reliability calculation. The results of construct validity analysis with 495 university education students showed that the scale consisted of four components: Physics course/test anxiety, anxiety about lack of physics knowledge, mathematics anxiety, and physics laboratory anxiety. The Cronbach’s alpha reliability coefficient was found as . 95 for the whole scale and for the components it ranged from . 83 to . 92. Confirmatory factor analysis, using another sample of 864 university education students with similar characteristics as the previous sample suggested that the four factor model for the PARS is valid. Hence, each component displayed satisfactory internal consistency reliability. According to findings, the PARS may be a useful tool in identifying the anxiety of undergraduate students taking physics courses. It can be used to determine students’ physics anxiety in a particular course for instructional purposes or it can be used as a pre-and post-test to determine the change in students’ physics anxiety.
Mesozooplankton Grazing on Picocyanobacteria in the Baltic Sea as Inferred from Molecular Diet Analysis

Our current knowledge on the microbial component of zooplankton diet is limited, and it is generally assumed that bacteria-sized prey is not directly consumed by most mesozooplankton grazers in the marine food webs. We questioned this assumption and conducted field and laboratory studies to examine picocyanobacteria contribution to the diets of Baltic Sea zooplankton, including copepods. First, qPCR targeting ITS-1 rDNA sequence of the picocyanobacteria Synechococcus spp. was used to examine picocyanobacterial DNA occurrence in the guts of Baltic zooplankton (copepods, cladocerans and rotifers). All field-collected zooplankton were found to consume picocyanobacteria in substantial quantities. In terms of Synechococcus quantity, the individual gut content was highest in cladocerans, whereas biomass-specific gut content was highest in rotifers and copepod nauplii. Moreover, the gut content in copepods was positively related to the picocyanobacteria abundance and negatively to the total phytoplankton abundance in the water column at the time of sampling. This indicates that increased availability of picocyanobacteria resulted in the increased intake of this prey and that copepods may rely more on picoplankton when food in the preferred size range declines. Second, a feeding experiments with a laboratory reared copepod Acartia tonsa fed a mixture of the picocyanobacterium Synechococcus bacillaris and microalga Rhodomonas salina confirmed that copepods ingested Synechococcus, even when the alternative food was plentiful. Finally, palatability of the picocyanobacteria for A. tonsa was demonstrated using uptake of 13C by the copepods as a proxy for carbon uptake in feeding experiment with 13C-labeled S. bacillaris. These findings suggest that, if abundant, picoplankton may become an important component of mesozooplankton diet, which needs to be accounted for in food web models and productivity assessments.
Optimising Homing Endonuclease Gene Drive Performance in a Semi-Refractory Species: The Drosophila melanogaster Experience

Homing endonuclease gene (HEG) drive is a promising insect population control technique that employs meganucleases to impair the fitness of pest populations. Our previous studies showed that HEG drive was more difficult to achieve in Drosophila melanogaster than Anopheles gambiae and we therefore investigated ways of improving homing performance in Drosophila. We show that homing in Drosophila responds to increased expression of HEGs specifically during the spermatogonia stage and this could be achieved through improved construct design. We found that 3′-UTR choice was important to maximise expression levels, with HEG activity increasing as we employed Hsp70, SV40, vasa and βTub56D derived UTRs. We also searched for spermatogonium-specific promoters and found that the Rcd-1r promoter was able to drive specific expression at this stage. Since Rcd-1 is a regulator of differentiation in other species, it suggests that Rcd-1r may serve a similar role during spermatogonial differentiation in Drosophila. Contrary to expectations, a fragment containing the entire region between the TBPH gene and the bgcn translational start drove strong HEG expression only during late spermatogenesis rather than in the germline stem cells and spermatogonia as expected. We also observed that the fraction of targets undergoing homing was temperature-sensitive, falling nearly four-fold when the temperature was lowered to 18°C. Taken together, this study demonstrates how a few simple measures can lead to substantial improvements in the HEG-based gene drive strategy and reinforce the idea that the HEG approach may be widely applicable to a variety of insect control programs.
Inferring Internet denial-of-service activity

In this article, we seek to address a simple question: “How prevalent are denial-of-service attacks in the Internet? ” Our motivation is to quantitatively understand the nature of the current threat as well as to enable longer-term analyses of trends and recurring patterns of attacks. We present a new technique, called “backscatter analysis,” that provides a conservative estimate of worldwide denial-of-service activity. We use this approach on 22 traces (each covering a week or more) gathered over three years from 2001 through 2004. Across this corpus we quantitatively assess the number, duration, and focus of attacks, and qualitatively characterize their behavior. In total, we observed over 68,000 attacks directed at over 34,000 distinct victim IP addresses---ranging from well-known e-commerce companies such as Amazon and Hotmail to small foreign ISPs and dial-up connections. We believe our technique is the first to provide quantitative estimates of Internet-wide denial-of-service activity and that this article describes the most comprehensive public measurements of such activity to date.
Distributed MIMO Precoding for In-Band Full-Duplex Wireless Backhaul in Heterogeneous Networks

This paper investigates distributed MIMO precoding design to maximize the weighted sum rate in a heterogeneous network where the multiple input multiple output full-duplex (MIMO-FD) small cells reuse the downlink spectrum of the macro base-station (BS) to exchange backhaul information. The multi-antenna BS transmits signals to the cellular users using the dirty paper coding technique and the MIMO-FD small cells apply FD precoding structures to effectively balance the received signal, the self-interference (SI), and the co-channel interference (CCI). Since the optimization problem is shown to be nonconvex, obtaining the global optimum is challenging. A low-complexity solution with distributed implementation is introduced with proved convergence. By applying the successive convex approximation technique and the duality between the broadcast channel and the multiple access channel, the original nonconvex problem is decomposed into a sequence of convex subproblems, which can be solved analytically and separately at each small cell and macro BS with limited channel state information exchange. Simulation results confirm the convergence and demonstrate the benefits of the introduced algorithm. It is shown that the SI and CCI can be suppressed effectively with sufficient cancellation power and number of transmit antennas at the FD small cells.