Miracle-dz/UniFAR-FTUs huggingface dataset:
Arsenite Induces Apoptosis of Murine T Lymphocytes Through Membrane Raft-Linked Signaling for Activation of c-Jun Amino-Terminal Kinase1

Because of its dual roles in acute toxicity and in therapeutic application in cancer treatment, arsenic has recently attracted a renewed attention. In this study, we report NaAsO2-induced signal cascades from the cell surface to the nucleus of murine thymic T lymphocytes that involve membrane rafts as an initial signal transducer. NaAsO2 induced apoptosis through fragmentation of DNA, activation of caspase, and reciprocal regulation of Bcl-2/Bax with the concomitant reduction of membrane potential. We demonstrated that NaAsO2-induced caspase activation is dependent on curcumin-sensitive c-Jun amino-terminal kinase and barely dependent on SB203580-sensitive p38 kinase or PD98059-sensitive extracellular signal-regulated kinase. Additionally, staurosporine, which severely inhibited the activation of mitogen-activated protein (MAP) family kinases and c-Jun, partially blocked the NaAsO2-mediated signal for poly(ADP-ribose) polymerase (PARP) degradation. Potentially as the initial cell surface event for intracellular signaling, NaAsO2 induced aggregation of GPI-anchored protein Thy-1 and superoxide production. This Thy-1 aggregation and subsequent activation of MAP family kinase and c-Jun and the degradation of PARP induced by NaAsO2 were all inhibited by DTT, suggesting the requirement of interaction between arsenic and protein sulfhydryl groups for those effects. β cyclodextrin, which sequestrates cholesterol from the membrane rafts, inhibited NaAsO2-induced activation of protein tyrosine kinases and MAP family kinases, degradation of PARP, and production of superoxide. In addition, β cyclodextrin dispersed NaAsO2-induced Thy-1 clustering. These results suggest that a membrane raft integrity-dependent cell surface event is a prerequisite for NaAsO2-induced protein tyrosine kinase/c-Jun amino-terminal kinase activation, superoxide production, and downstream caspase activation.
ETHNOMEDICINAL REVIEW OF FOLKLORE MEDICINAL PLANTS BELONGING TO FAMILY APIACEAE OF PAKISTAN

The use of herbs for therapeutic purpose is as old as human history. In Pakistan a major part of population is dependent on the traditional medicine derived from plants for primary health care system. The interest in the use of traditional system of medicine has gained popularity globally. The developed countries are shifting their focus to further research based on the indigenous knowledge collected from aboriginal people. The present study reviews the ethno-medicinal uses of family Apiaceae reported from Pakistan. Out of 167 species reported from Pakistan, 66 are found to be used medicinally. Most commonly treated disorders by use of Apiaceae herbal flora are gastrointestinal tract and liver disorders (28%) followed by cough, cold and respiratory tract problems (11%). The plant parts frequently used are roots (22%) followed by whole plant material (19%), leaf material (18%), fruit (13%), seed (12%), stem, flower, aerial parts (5%) and sap (1%). It is suggested to carry out similar studies for other families to explore the indigenous knowledge for the development of commercial products and to collectively document the scattered existing knowledge.
Using principal curvatures and Darboux frame to recover 3D geometric primitives from range images

We present a method for the recovery of partially occluded 3D geometric primitives from range images which might also include nonprimitive objects. The method uses a technique for estimating the principal curvatures and Darboux frame from range images which we developed. After estimating the principal curvatures and the Darboux frames from the entire scene, a search for the known patterns of these features in geometric primitives is performed. If a specific pattern is identified then the presence of the corresponding primitive is confirmed using these local features. The features are also used to recover the primitive's characteristics. The suggested application is very efficient since it combines the segmentation, classification and fitting processes, which are part of any recovery process, in a single process, which advances monotonously through the recovery procedure. The combined process does not use any least-squares fittings and therefore is very robust to inaccuracies in the local feature extraction process and to errors in segmentation. It was tested on series of real complex cluttered scenes, yielding accurate and robust recoveries of primitives.
Toward All Room‐Temperature, Solution‐Processed, High‐Performance Planar Perovskite Solar Cells: A New Scheme of Pyridine‐Promoted Perovskite Formation

A new, all room-temperature solution process is developed to fabricate efficient, low-cost, and stable perovskite solar cells (PVSCs). The PVSCs show high efficiency of 17.10% and 14.19%, with no hysteresis on rigid and flexible substrates, respectively, which are the best efficiencies reported to date for PVSCs fabricated by room-temperature solution-processed techniques. The flexible PVSCs show a remarkable power-per-weight of 23.26 W g-1 .
Malformation syndromes--a diagnostic approach.

Seven in a thousand children are born with multiple malformations:' many of them will have one of the thousand or so malformation syndromes that have been described in the published reports. All malformation syndromes are rare and it is unlikely that the average clinician, or even the experienced dysmorphologist, will be able to recall all of them and to keep up to date with new reports. Nevertheless, a correct diagnosis is essential before recurrence risks and prognosis can be assessed.
Misbehavior analysis of IEEE 802.11 MAC layer in mobile ad hoc network using stochastic reward nets

In this paper, we present a Petri net model for performance evaluation of IEEE 802.11 distributed coordination function as a popular media access control layer protocol in mobile ad hoc network. The goal of this evaluation is to examine this protocol under the existing of misbehavior nodes that selfishly try to grasp common channel in a neighbor area. The presented model consists of 2 separate models based on stochastic reward net (SRN), as a variation of stochastic Petri net. The first model, which is called one node operation model, is supposed for presenting all distributed coordination function operations in a single node such as collision avoidance, request to send/clear to send (RTS/CTS) handshake, and backoff mechanism. The next SRN model, all node operation model, is used for modeling nodes competition for occupying channel in a neighbor area. The models could be adjusted to a dynamic network with any number of nodes, dimension scale, and nodes' speed. For evaluation purpose, 4 distinct attack types implemented by modifying associated transitions in SRN models. The proposed SRN model has been quantified by deriving 2 performances metrics as Throughput and Delay. Both metrics are also compared to the value obtained from NS‐2 in terms of different number of nodes and 3 packet generation rates. Three additional metrics measuring the channel usage are also quantified in terms of different attack strategies using only presented SRN model.
Response to Comment on “Cutting Edge: Human CD4−CD8− Thymocytes Express FOXP3 in the Absence of a TCR”

W e thank Battaglia and colleagues (1) for their interest in our work (2). However, contrary to their claim, CD3 is not a fully reliable surrogate for TCR on thymocytes, and surface CD3 is not always associated with a TCR. Most notably, early thymocytes express low levels of surface CD3 together with pre-TCR before TCR locus rearrangement (3). We did not detect pre-TCR on FOXP3 DN thymocytes, but the intensity of staining with the noncommercial anti-preT mAb was low and establishing the status of pre-TCR expression was not the focus of our study. As regards the antiTCR mAb, we are not sure what Battaglia et al. mean by “scarcely efficient reagent” (1). We are not aware of any particular problems with the widely used WT31 clone, and we did not find it unduly difficult to assign both FOXP3 and FOXP3 thymocytes to TCR , TCR, and TCR subsets (Fig. 1 in Ref. 2). Perhaps Battaglia et al. refer to the known propensity of WT31 to cross-react with an epitope formed by TCR and CD3 (4), but we fail to see how in the present context this could be a source of error. Arguing against the functional expression of an TCR is also the fact that the FOXP3 DN thymocytes did not express CD5 or CD69, molecules up-regulated in response to TCR signaling (2). Apart from the divergence of using anti-CD3 instead of antiTCR mAb, Battaglia et al. (1) found a much higher frequency of FOXP3 cells within the DN population than we did (2), their mean value (6.1%) lying altogether outside our range of observations (0.1–3.8%). This discrepancy also suggests either patient-related differences or different methodology. We note that Battaglia and colleagues (5) have used the PCH101 antiFOXP3 mAb, recently suggested to bind nonspecifically to activated T cells (6). Thymocytes at different developmental stages are heterogeneous in terms of metabolic activity and cell cycle status, and it is not known whether some of them display similar nonspecific binding. This raises the possibility that some fraction of the FOXP3 DN cells observed by Battaglia et al. might in fact not express FOXP3. Finally, we wonder why Battaglia et al. conclude that FOXP3 expression is restricted to CD3 cells (legend to Fig. 1 in Ref. 1), when the representative figure itself seems to indicate that some of the FOXP3 DN thymocytes are indeed CD3 (1). A plausible synthesis of the two data sets (1, 2) might thus be that the FOXP3 DN thymocytes can be divided into CD3 TCR , CD3pre-TCR , and CD3TCR populations. These stages would also form a logical and theoretically consistent progression toward the FOXP3 TCR thymocytes found in the CD4 CD8 population. Our conclusion remains unchanged: the up-regulation of FOXP3 in human thymocytes precedes TCR expression.
Live demonstration: A 128-channel spike sorting processor featuring 0.175 μW and 0.0033 mm2 per Channel in 65-nm CMOS

Multi-electrode intracranial recording technology is highly required for various applications such as brain studies, brain machine interface (BMI) and treatment of disorders like epilepsy, memory loss and paralysis. The recording is done by inserting electrodes into the extracellular tissue of the brain to supposedly record the single-unit activity. However, the recorded signal is the summation of some near-by neurons activities and the background noise. Therefore, after recording and digitizing the signal by analog front-end, the first crucial step is to extract the information from extracellular recording [1]. This process is called spike sorting and shown in Fig. 1. It basically assigns the detected spike to their source neurons located near the corresponding recording electrodes.
Tracking Control for Switched Linear Systems with Time-Delay

Abstract Tracking control for switched linear systems with time-delay is investigated in this paper. Sufficient conditions for the solvability of the tracking control problem are given respectively for the cases that the state of system is measurable and unmeasurable. When the state is measurable, we design a switching control law to achieve the H∞ model reference tracking performance. When the state is not available, the design of a switching control law based on measured output instead of the state information is considered. Lyapunov function methods are utilized to the stability analysis and controller design for the switched linear systems with time-delay. By using linear matrix inequalities and convex optimization techniques, the controller design problem can be solved efficiently. The simulation examples show the validity of the switching control laws.
Criterion validity of lower extremity Motricity Index scores

Objective: To examine the criterion validity of lower extremity Motricity Index scores. Design: Retrospective cross-sectional comparison of lower extremity Motricity Index scores and hand-held dynamometer measurements obtained from 15 patients with stroke. Results: For individual actions (ankle dorsiflexion, knee extension and hip flexion) and all actions combined, Pearson correlations were good to excellent (r = 0.78–0.91), significant (p < 0.001), and of high power (9%). Conclusions: The findings of this study support the criterion validity of the lower extremity Motricity Index.
Shaping online learning communities and the way adaptiveness adds to the picture

With learning being a process closely connected to sociability, learning on the web is in many cases accompanied and promoted by the creation and maintenance of online communities. Even though today's web-based learning environments have drastically evolved and now incorporate techniques from other domains and application areas (such as web mining, AI, user modelling, and profiling), setting up a successful online learning community is not a trivial task. Experience has indicated that the road from assuring all technical prerequisites to having people participating and keeping the community "alive", is long and winding. This paper argues that by monitoring the behaviour of community members, their expertise, skills, opinions and/or preferences and requirements and by applying certain adaptation mechanisms, the experience and effectiveness of online learning can be significantly improved.
The MEK1 Proline-rich Insert Is Required for Efficient Activation of the Mitogen-activated Protein Kinases ERK1 and ERK2 in Mammalian Cells*

MEK1 and MEK2 contain a proline-rich insert not present in any other known MEK (MAP (mitogen-activated protein)/ERK (extracellular signal-regulated kinase) kinase) family members. We examined the effect of removing the MEK1 polyproline insert on MEK activity, its binding to Raf, and its ability to activate ERKs in cells. Deletion of the insert had no effect on either the activity of MEK1 or on its ability to bind to Raf-1. Both wild type and constitutively active MEK1 coimmunoprecipitated with Raf-1 whether or not the insert was present. Deletion of the insert did not reduce activation of MEK1 by EGF or activated Raf in cells. The proline-rich insert enhanced the ability of an otherwise equally active MEK1 protein to regulate endogenous ERKs in mammalian cells. Overexpression of either constitutively active MEK1 lacking the insert or ERK2 compensates for the weaker in vivo activity of the MEK1 deletion mutant. Expression of the insert in cells reduced activation of ERKs by EGF. We conclude that the proline-rich insert is not the site of the MEK-Raf interaction and that the polyproline insert is required for its efficient activation of downstream ERKs in cells.
Protective immunity induced with 23 kDa membrane protein dna vaccine of Schistosoma japonicum Chinese strain in infected C57BL/6 mice.

A 23 kDa membrane protein DNA vaccine for Schistosoma japonicum Chinese strain was developed and tested for its protective efficacy and immune responses in infected C57BL/6 mice. The cDNA encoding SjC23 amplified from pUC19-SjC23 were subcloned into an eukaryotic expression vector (pcDNA3.1). Forty-eight female C57BL/6 mice were divided into three groups. Each mouse of group A (control group) was immunized intramuscularly (i.m.) with 100 microg of pcDNA3.1; of group B (SjC23 group) was immunized (i.m.) with 100 microg of pcDNA3.1-SjC23; of group C (SjC23+IL-12) was immunized (i.m.) with a mixture of 100 microg of pcDNA3.1-SjC23, 100 microg of pcDNA3.1-p35 and 100 microg of pcDNA-p40. These were followed by two boosts of the same DNA once every two weeks. All mice were challenged with 45 cercariae of Schistosoma japonicum Chinese strain at week 8, and were killed and perfused at week 14. The numbers of recovered worms and hepatic eggs were counted. The expression of SjC23 and p35, p40 in muscle tissue was determined by immunohistochemical method. By culture of spleen cells, the production of IL-2, IL-4, IL-10 and IFN-gamma with the stimulation of specific antigen of the recombinant hydrophilic domain of SjC23 (rSjC23-HD) was determined after the last immunization (before challenge). Sera were collected from each group before immunization and two weeks before and after challenge. Anti-SjC23 antibodies were tested by Western blot. The results showed that SjC23 and p35, p40 of mouse IL-12 were expressed on the membrane and in the plasma of the muscle cells of immunized C57BL/6 mice. A rise of IL-2 and IFN-gamma in the SjC23 group and SjC23+IL-12 group was observed; No changes were found in IL-4 and IL-10. Detection of anti-SjC23 antibody with Western blot showed that after the third immunization (before challenge) all the serum samples from the control group were negative; 8 of 10 sera from the SjC23 group and 9 of 10 sera from the SjC23+IL-12 group were positive. The worm reduction rates in the SjC23 group and SjC23+IL-12 group were 26.9% and 35.4% respectively; the liver eggs reduction rates were 22.2% and 28.4%, respectively in comparison to the control group. This indicates that the pcDNA3.1-SjC23 DNA vaccine can induce partial protection against Schistosoma japonicum infection in C57BL/6 mice.
Clinical Trial

A number of such antiseptics are available, of which the hydroxyquinoline group are the 1110~t widely used. Various a(kantagcs arc c! a1111ed for individual members of the group and it was thought that a comparison might he of some interest. to sec if anv difference could be shown in normal clinic;! usage. An unselected series of patients with dermatoses requiring treatment with such steroid combinatio~ creams were given both iodochlorhydroxyqumoline 3 per cent with hydrocortisone 1 per cent (' Vioform' hydrocortisone, CIBA) and standardized chlorhydroxyquinolines 0. 75 per cent with triamcinolone acetonide 0.025 per cent (· Remiderm ', Squibb) in a random order and the results assessed.
FACTOR SCREENING AND RESPONSE SURFACE EXPLORATION

Standard practice in response surface methodology performs factor screen- ing and response surface exploration sequentially, using different designs. A novel approach is proposed to achieve the two objectives on the same experiment, based on one design. Running a uni-stage experiment has the advantages of saving ex- perimentation time and run size. The approach is based on a two-stage anal- ysis that employs factor screening, projection and response surface exploration. Projection-efficiency criteria are defined to evaluate the performance of the pro- jected designs. The projection-efficiency properties of the 3 n−k designs and three nonregular designs are studied, and comparisons with central composite designs are made. Nonregular designs appear to enjoy better projection properties. The strategy is illustrated with the analysis of a PVC insulation experiment.
Architecture of the Photosynthetic Oxygen-Evolving Center

Photosynthesis uses light energy to drive the oxidation of water at an oxygen-evolving catalytic site within photosystem II (PSII). We report the structure of PSII of the cyanobacterium Thermosynechococcus elongatus at 3.5 angstrom resolution. We have assigned most of the amino acid residues of this 650-kilodalton dimeric multisubunit complex and refined the structure to reveal its molecular architecture. Consequently, we are able to describe details of the binding sites for cofactors and propose a structure of the oxygen-evolving center (OEC). The data strongly suggest that the OEC contains a cubane-like Mn3CaO4 cluster linked to a fourth Mn by a mono-μ-oxo bridge. The details of the surrounding coordination sphere of the metal cluster and the implications for a possible oxygen-evolving mechanism are discussed.
Profile likelihood in systems biology

Inferring knowledge about biological processes by a mathematical description is a major characteristic of Systems Biology. To understand and predict system's behavior the available experimental information is translated into a mathematical model. Since the availability of experimental data is often limited and measurements contain noise, it is essential to appropriately translate experimental uncertainty to model parameters as well as to model predictions. This is especially important in Systems Biology because typically large and complex models are applied and therefore the limited experimental knowledge might yield weakly specified model components. Likelihood profiles have been recently suggested and applied in the Systems Biology for assessing parameter and prediction uncertainty. In this article, the profile likelihood concept is reviewed and the potential of the approach is demonstrated for a model of the erythropoietin (EPO) receptor.
Comparison of application of the ACC/AHA guidelines, Adult Treatment Panel III guidelines, and European Society of Cardiology guidelines for cardiovascular disease prevention in a European cohort.

IMPORTANCE The 2013 American College of Cardiology/American Heart Association (ACC/AHA) guidelines introduced a prediction model and lowered the threshold for treatment with statins to a 7.5% 10-year hard atherosclerotic cardiovascular disease (ASCVD) risk. Implications of the new guideline's threshold and model have not been addressed in non-US populations or compared with previous guidelines. OBJECTIVE To determine population-wide implications of the ACC/AHA, the Adult Treatment Panel III (ATP-III), and the European Society of Cardiology (ESC) guidelines using a cohort of Dutch individuals aged 55 years or older. DESIGN, SETTING, AND PARTICIPANTS We included 4854 Rotterdam Study participants recruited in 1997-2001. We calculated 10-year risks for "hard" ASCVD events (including fatal and nonfatal coronary heart disease [CHD] and stroke) (ACC/AHA), hard CHD events (fatal and nonfatal myocardial infarction, CHD mortality) (ATP-III), and atherosclerotic CVD mortality (ESC). MAIN OUTCOMES AND MEASURES Events were assessed until January 1, 2012. Per guideline, we calculated proportions of individuals for whom statins would be recommended and determined calibration and discrimination of risk models. RESULTS The mean age was 65.5 (SD, 5.2) years. Statins would be recommended for 96.4% (95% CI, 95.4%-97.1%; n = 1825) of men and 65.8% (95% CI, 63.8%-67.7%; n = 1523) of women by the ACC/AHA, 52.0% (95% CI, 49.8%-54.3%; n = 985) of men and 35.5% (95% CI, 33.5%-37.5%; n = 821) of women by the ATP-III, and 66.1% (95% CI, 64.0%-68.3%; n = 1253) of men and 39.1% (95% CI, 37.1%-41.2%; n = 906) of women by ESC guidelines. With the ACC/AHA model, average predicted risk vs observed cumulative incidence of hard ASCVD events was 21.5% (95% CI, 20.9%-22.1%) vs 12.7% (95% CI, 11.1%-14.5%) for men (192 events) and 11.6% (95% CI, 11.2%-12.0%) vs 7.9% (95% CI, 6.7%-9.2%) for women (151 events). Similar overestimation occurred with the ATP-III model (98 events in men and 62 events in women) and ESC model (50 events in men and 37 events in women). The C statistic was 0.67 (95% CI, 0.63-0.71) in men and 0.68 (95% CI, 0.64-0.73) in women for hard ASCVD (ACC/AHA), 0.67 (95% CI, 0.62-0.72) in men and 0.69 (95% CI, 0.63-0.75) in women for hard CHD (ATP-III), and 0.76 (95% CI, 0.70-0.82) in men and 0.77 (95% CI, 0.71-0.83) in women for CVD mortality (ESC). CONCLUSIONS AND RELEVANCE In this European population aged 55 years or older, proportions of individuals eligible for statins differed substantially among the guidelines. The ACC/AHA guideline would recommend statins for nearly all men and two-thirds of women, proportions exceeding those with the ATP-III or ESC guidelines. All 3 risk models provided poor calibration and moderate to good discrimination. Improving risk predictions and setting appropriate population-wide thresholds are necessary to facilitate better clinical decision making.