Miracle-dz/UniFAR-FTUs huggingface dataset:
CAT: Contention Aware Transport Protocol for IEEE 802.11 MANETs

In this paper, we present a contention aware transport (CAT) protocol which is hop-by-hop, rate-based control, over IEEE 802.11 MANETs. CAT introduces a novel control metric, sending rate control factor (SRCF), for the congestion control. The SRCF considers the contention density which represents the degree of contention level experienced at a given node. In addition, to support reliable delivery, CAT uses a hop-by-hop acknowledgement scheme. The main purpose of CAT is, to find optimal traffic load that the channel bandwidth is fully utilized by sending rate adjustment while minimizing the packet losses from medium contention. The simulation results show that the network throughput achieved by CAT is around 10% and about 30% at peak point, higher than that of TCP and TCP-SACK
With a little help from my friends: examining the impact of social annotations in sensemaking tasks

In prior work we reported on the design of a social annotation system, SparTag.us, for use in sensemaking activities such as work-group reading and report writing. Previous studies of note-taking systems have demonstrated behavioral differences in social annotation practices, but are not clear in the actual performance gains provided by social features. This paper presents a laboratory study aimed at evaluating the learning effect of social features in SparTag.us. We found significant learning gains, and consider implications for design and for understanding the underlying mechanisms in play when people use social annotation systems.
Biological Weighting Function for the Inhibition of Phytoplankton Photosynthesis by Ultraviolet Radiation

Severe reduction of stratospheric ozone over Antarctica has focused increasing concern on the biological effects of ultraviolet-B (UVB) radiation (280 to 320 nanometers). Measurements of photosynthesis from an experimental system, in which phytoplankton are exposed to a broad range of irradiance treatments, are fit to an analytical model to provide the spectral biological weighting function that can be used to predict the short-term effects of ozone depletion on aquatic photosynthesis. Results show that UVA (320 to 400 nanometers) significantly inhibits the photosynthesis of a marine diatom and a dinoflagellate, and that the effects of UVB are even more severe. Application of the model suggests that the Antarctic ozone hole might reduce near-surface photosynthesis by 12 to 15 percent, but less so at depth. The experimental system makes possible routine estimation of spectral weightings for natural phytoplankton.
Pre bonding metrology solutions for 3D integration

This article reports the capability and the recent development of optical profilometry for monitoring 3D integrated circuits. In particular, the capability to profile transparent film stacks, which was quite challenging, is now accessible with the Unifire optical profilometer from Nanometrics. It is demonstrated that the obtained information in term of topography and edge roll off is paramount to improving the 3D integration process. In addition, the implementation of Nanometrics' Advanced Film Capability (AFC) and/or Index Corrected Topography (ICT) may enable more detailed mapping of local within die film thickness and topography respectively.
Allele-Specific Knockdown of ALS-Associated Mutant TDP-43 in Neural Stem Cells Derived from Induced Pluripotent Stem Cells

TDP-43 is found in cytoplasmic inclusions in 95% of amyotrophic lateral sclerosis (ALS) and 60% of frontotemporal lobar degeneration (FTLD). Approximately 4% of familial ALS is caused by mutations in TDP-43. The majority of these mutations are found in the glycine-rich domain, including the variant M337V, which is one of the most common mutations in TDP-43. In order to investigate the use of allele-specific RNA interference (RNAi) as a potential therapeutic tool, we designed and screened a set of siRNAs that specifically target TDP-43M337V mutation. Two siRNA specifically silenced the M337V mutation in HEK293T cells transfected with GFP-TDP-43wt or GFP-TDP-43M337V or TDP-43 C-terminal fragments counterparts. C-terminal TDP-43 transfected cells show an increase of cytosolic inclusions, which are decreased after allele-specific siRNA in M337V cells. We then investigated the effects of one of these allele-specific siRNAs in induced pluripotent stem cells (iPSCs) derived from an ALS patient carrying the M337V mutation. These lines showed a two-fold increase in cytosolic TDP-43 compared to the control. Following transfection with the allele-specific siRNA, cytosolic TDP-43 was reduced by 30% compared to cells transfected with a scrambled siRNA. We conclude that RNA interference can be used to selectively target the TDP-43M337V allele in mammalian and patient cells, thus demonstrating the potential for using RNA interference as a therapeutic tool for ALS.
Studying Phenotypic Variability in Crops using a Hand-held Sensor Platform

Recent developments in visual-inertial and LiDAR sensors and simultaneous localization and mapping (SLAM) enable recording and digital reconstruction of the physical world. In this paper we utilize a hand-held multi-sensor platform for remotely recording and characterizing physical properties of crops on a field. The platform consists of a visual-inertial sensor, color camera and 2D LiDAR. We syncronize the data from this platform and fuse them in a standard SLAM framework to obtain a detailed model of the field environment in the form of a 3D point cloud. Such a model is then fed into semi-automated crop parameter estimation pipelines to extract the spatio-temporal variation of physical crop height and canopy cover, which may be used to support decision making for breeding and precision agriculture. We present experimental results with data collected on a winter wheat field in Eschikon, Switzerland, showing the utility of our approach towards automating variability studies in crops.
A Game-Theoretic Model of Disclosure–Donation Interactions in the Market for Charitable Contributions

The information organizations choose to disclose is a strategic consideration. The “success” of strategic disclosure is contingent in turn on the target audience's values and preferences. The disclosure of and reaction to organizational information thus involves a strategic interaction between the producer and consumer of the information, yet prior communication research has focused on only one side or the other of this equation. In response, we examine organization–public interactions in a domain with key, measurable outcomes—the charitable donations marketplace—and propose a game-theoretic explanation of organizational disclosures and individual donations. The study specifically emphasizes two core donor preferences—the desire for impact and the desire for publicity—with donors choosing between organizations based on how well the organization satisfies these preferences. Organizations’ optimal level of disclosure, in turn, depends on their own “type” and the types of donors they attract. This study recommends organizations think of their disclosure and efficiency-related decisions as conveying valuable, yet distinct, information to two ideal-types of prospective donors: the impact maximizer and the publicity maximizer. Mapping and targeting the “right” mix of donors is a key managerial decision that ultimately impacts both the organization's financial outcomes and donors' satisfaction with the donation experience.
Optimal management of cervical cancer in HIV-positive patients: a systematic review

The clinical management of cervical cancer in HIV‐positive patients has challenges mainly due to the concerns on immune status. At present, their mode of management is similar to HIV‐seronegative patients involving the use of chemotherapy and radiotherapy concurrently as indicated. HIV infection, cancer, radiotherapy, and chemotherapy lower immunity through reduction in CD4 cell counts. At present there are no treatment guidelines for HIV‐positive patients. This study was done to systematically review the literature on cervical cancer management in HIV‐positive patients and treatment outcomes. A systematic literature search was done in the major databases to identify studies on the management of HIV‐positive patients with cervical cancer. Identified studies were assessed for eligibility and inclusion in the review following the guidelines of The Cochrane Handbook for Systematic Reviews and CRD's (Centre for Reviews and Dissemination) guidance for undertaking reviews in health care. Eight eligible studies were identified from the literature. Three of them were prospective while five were retrospective studies. Notably, the average age at diagnosis of cervical cancer in HIV‐positive patients was a decade lower than in seronegative patients. There was no difference in distribution of stages of disease at presentation between HIV‐positive and negative patients. Mild acute toxicity (Grades 1 and 2) was higher in HIV‐positive patients than in HIV‐negative patients in hematopoietic system. In the grades 3 and 4 reactions, anemia was reported in 4% versus 2% while gastrointestinal reactions were reported in 5% versus 2% respectively. In general, patients who were started early on HAART had higher rates of treatment completion. The study supports the suggestion that HAART should be commenced early at cervical cancer diagnosis in HIV‐positive patients diagnosed with cervical cancer to ensure less toxicity and better treatment compliance.
Integrated grasp and motion planning using independent contact regions

Traditionally, grasp and arm motion planning are considered as separate tasks. This paper presents an integrated approach that only requires the initial configuration of the robotic arm and the pose of the target object to simultaneously plan a good hand pose and arm trajectory to grasp the object. The planner exploits the concept of independent contact regions to look for the best possible grasp. The goal poses for the end effector are obtained using two different methods: one that biases a sampling approach towards favorable regions using principal component analysis, and another one that considers the capabilities of the robotic arm to decide the most promising hand poses. The proposed method is evaluated using different scenarios for the humanoid robot Spacejustin.
Influence of years since menopause on bone mineral metabolism in South Indian women.

BACKGROUND Although an increase of bone turnover has been documented at the time of menopause, the subsequent abnormalities of bone resorption and formation in the elder women have not been investigated. AIM To assess bone turnover among different YSM (years since menopause) groups of postmenopausal women. SETTINGS AND DESIGN A case control study in a tertiary care hospital. MATERIALS AND METHODS Forty-seven premenopausal (control) women and 257 postmenopausal women were included in this study. Based on YSM, the postmenopausal women were divided into four groups namely, 1-5 YSM (n = 82), 6-10 YSM (n = 77), 11-15 YSM (n = 58) and > 15 YSM (n = 40). The levels of calcium, phosphorus, total alkaline phosphatase, FSH, LH, estradiol, intact-paratharmone and 25-hydroxy vitamin D in serum and urine levels of calcium, phosphorus and bone resorption marker calcium/creatinine(Ca/Cre) ratios were analyzed in all subjects. STATISTICAL ANALYSIS USED One way ANOVA followed by Duncan's multiple range test. RESULTS Significantly increased levels of FSH (P < 0.001) and declined levels of urine calcium (P = 0.015) and Ca/Cre ratios (P = 0.006) were observed in > 15 YSM group over 1-5 and 6-10 YSM groups. An inverse correlation was observed between serum FSH levels and urine Ca/Cre ratios (r = -0.655, P < 0.001) in > 15 YSM group. Comparable deficient estradiol levels were observed in all YSM groups. CONCLUSIONS The risk of bone resorption is greater in early years than late years of menopause. The decreased bone resorption risk in late postmenopausal women might be due to increased FSH levels. However, further studies are required to explore this finding.
SPX4 Negatively Regulates Phosphate Signaling and Homeostasis through Its Interaction with PHR2 in Rice[W][OPEN]

This study shows that rice SPX4 negatively regulates phosphate signaling and homeostasis through its interaction with PHR2, a key transcription factor regulating phosphate signaling. SPX4 stabilization is dependent on phosphate concentration and appears to act as a regulatory point both for nuclear localization and for binding of PHR2 to P1BS cis-elements in target DNA. PHR2, a central regulator of phosphate signaling in rice, enhanced the expression of phosphate starvation-induced (PSI) genes and resulted in the enhancement of Pi acquisition under Pi deficiency stress. This occurred via PHR2 binding to a cis-element named the PHR1 binding sequences. However, the transcription level of PHR2 was not responsive to Pi starvation. So how is activity of transcription factor PHR2 adjusted to adapt diverse Pi status? Here, we identify an SPX family protein, Os-SPX4 (SPX4 hereafter), involving in Pi starvation signaling and acting as a negative regulator of PHR2. SPX4 is shown to be a fast turnover protein. When Pi is sufficient, through its interaction with PHR2, SPX4 inhibits the binding of PHR2 to its cis-element and reduces the targeting of PHR2 to the nucleus. However, when plants grow under Pi deficiency, the degradation of SPX4 is accelerated through the 26S proteasome pathway, thereby releasing PHR2 into the nucleus and activating the expression of PSI genes. Because the level of SPX4 is responsive to Pi concentration and SPX4 interacts with PHR2 and regulates its activity, this suggests that SPX4 senses the internal Pi concentration under diverse Pi conditions and regulates appropriate responses to maintain Pi homeostasis in plants.
Inapproximability of the Tutte polynomial

The Tutte polynomial of a graph G is a two-variable polynomial T(G;x,y) that encodes many interesting properties of the graph. We study the complexityof the following problem, for rationals x and y: take as input a graph G, and output a value which is a good approximation to T(G;x,y). We are interested in determining for which points (x,y) there is a fullypolynomial randomised approximation scheme (FPRAS) for T(G;x,y). Our main contribution is a substantial widening of the region known to benon-FPRASable.
Efficient channel estimation of MIMO-OFDM system using pilot tones

An efficient method of channel estimation in MIMO-OFDM system is to use training symbols or pilots transmitted along with data sub-carriers. However these pilots cause inter-antenna interference when transmitted simultaneously from transmitting antennas. The use of null sub-carriers mitigates this but at the cost of spectral efficiency. This paper proposes an efficiency enhancing method in which the estimation of the channel at the receiver is done by adding the signals coming from different transmitters. The performance of the proposed method is evaluated using MATLAB.
A Vector Library for Silencing Central Carbon Metabolism Genes with Antisense RNAs in Escherichia coli

ABSTRACT We describe here the construction of a series of 71 vectors to silence central carbon metabolism genes in Escherichia coli. The vectors inducibly express antisense RNAs called paired-terminus antisense RNAs, which have a higher silencing efficacy than ordinary antisense RNAs. By measuring mRNA amounts, measuring activities of target proteins, or observing specific phenotypes, it was confirmed that all the vectors were able to silence the expression of target genes efficiently. Using this vector set, each of the central carbon metabolism genes was silenced individually, and the accumulation of metabolites was investigated. We were able to obtain accurate information on ways to increase the production of pyruvate, an industrially valuable compound, from the silencing results. Furthermore, the experimental results of pyruvate accumulation were compared to in silico predictions, and both sets of results were consistent. Compared to the gene disruption approach, the silencing approach has an advantage in that any E. coli strain can be used and multiple gene silencing is easily possible in any combination.
Modeling of Stock Markets with Mean Reversion

In this article we present a method for modeling and estimating the stock market with a mean reverting characteristic. Mean reversion is the tendency for the market to move back to an equilibrium level. The random walk description of stock markets has certain inaccuracies as such a process may diverge over time, resulting in negative or infinite values. There is no longer an acceptable model which can be effectively used to simulate the stock market. However, the mean reverting property exhibited by financial markets has been recognized by theorists. We analyze two methods of estimating the parameters of the model, Least Square Estimation and Maximum Likelihood Estimation. Using monthly data of the Dow Jones Industrial Average and the Singapore Straits Times Index, we compare the performance of these two methods.
Circuit model for resonant cavity mode enabled wireless power transfer

Recently, a new paradigm in wireless power transfer based on cavity mode resonance has experimentally shown the ability to efficiently deliver power to multiple receivers over large 3D volumes of an enclosed metallic cavity. However, existing analytical models based on coupled mode theory and finite element simulation tools are complicated to use, relatively slow to converge, and fail to give researchers and system designers the intuition to optimize wireless power transfer performance. In this work a general circuit model for the cavity resonant wireless power system is introduced and validated against simulated and measured results. Results show an average agreement between the circuit model and measured transfer efficiency are within +/−5%. Thus, cavity mode enabled wireless power transfer can be analyzed with an equivalent circuit model allowing for fast design iteration and a better understanding of how to optimize system performance. We used the circuit model developed herein to design a simple impedance matching network for 52 LED receivers and transferred power wirelessly to all of them simultaneously with approximately 30% efficiency, by combining two cavity modes, TE011 and TE012. However, under optimal load condition, which requires more complicated matching circuit, a minimum efficiency of 50% can easily be achieved at the same positions, we instead here we focused on a simple and fast design solution.
Association of tumor necrosis factor genetic polymorphism with chronic atrophic gastritis and gastric adenocarcinoma in Chinese Han population.

AIM To investigate the association of TNF polymorphisms with chronic atrophic gastritis (CAG) and gastric adenocarcinoma in Chinese Han patients. METHODS The TNFa-e 5 microsatellites and 3 RFLP sites were typed using PCR technique, followed by high-voltage denaturing PAGE with silver staining and restriction enzyme digestion respectively in specimens from 53 patients with CAG and 56 patients with gastric adenocarcinoma and 164 healthy controls. The PCR products were cloned and sequenced. RESULTS The frequency of TNF-beta Ncol*1/2 genotype was higher in patients with chronic atrophic gastritis than in healthy controls, but no significant difference was observed (60.38% vs 46.34%, P=0.076). The frequency of TNa10 allele was significantly higher in patients with chronic atrophic gastritis than in healthy controls (19.81% vs 11.89%, P=0.04). However, it did not relate to age, gender, atrophic degree or intestinal metaplasia in patients with chronic atrophic gastritis. The frequency of TNF-beta Ncol*1/2 and d2/d6 genotypes were significantly higher in patients with gastric adenocarcinoma than in healthy individuals (P>0.05). However, TNF-beta Ncol*1/2 and d2/d6 genotypes did not relate to age, gender, grade of differentiation and clinicopathologic stage in patients with gastric adenocarcinoma. The frequency of TNFa6b5c1 haplotype homozygote was significantly lower in patients with gastric adenocarcinoma than in healthy controls (1.79% vs 15.85%, P=0.006). CONCLUSION TNFa10 allele may be a risk factor for chronic atrophic gastritis. TNF-beta Ncol*1/2 and d2/d6 genotypes are associated with the susceptibility to gastric adenocarcinoma, whereas TNFa6b5c1 haplotype homozygote may contribute to the resistance against gastric adenocarcinoma.
STRING: known and predicted protein–protein associations, integrated and transferred across organisms

A full description of a protein's function requires knowledge of all partner proteins with which it specifically associates. From a functional perspective, ‘association’ can mean direct physical binding, but can also mean indirect interaction such as participation in the same metabolic pathway or cellular process. Currently, information about protein association is scattered over a wide variety of resources and model organisms. STRING aims to simplify access to this information by providing a comprehensive, yet quality-controlled collection of protein–protein associations for a large number of organisms. The associations are derived from high-throughput experimental data, from the mining of databases and literature, and from predictions based on genomic context analysis. STRING integrates and ranks these associations by benchmarking them against a common reference set, and presents evidence in a consistent and intuitive web interface. Importantly, the associations are extended beyond the organism in which they were originally described, by automatic transfer to orthologous protein pairs in other organisms, where applicable. STRING currently holds 730 000 proteins in 180 fully sequenced organisms, and is available at http://string.embl. de/.
A physiological strain index to evaluate heat stress.

A physiological strain index (PSI), based on rectal temperature (Tre) and heart rate (HR), capable of indicating heat strain online and analyzing existing databases, has been developed. The index rates the physiological strain on a universal scale of 0-10. It was assumed that the maximal Tre and HR rise during exposure to exercise heat stress from normothermia to hyperthermia was 3°C (36.5-39.5°C) and 120 beats/min (60-180 beats/min), respectively. Tre and HR were assigned the same weight functions as follows: PSI = 5(Tret - Tre0) ⋅ (39.5 - Tre0)-1+ 5(HR t - HR0) ⋅ (180 - HR0)-1, where Tret and HR t are simultaneous measurements taken at any time during the exposure and Tre0 and HR0 are the initial measurements. PSI was applied to data obtained from 100 men performing exercise in the heat (40°C, 40% relative humidity; 1.34 m/s at a 2% grade) for 120 min. A separate database representing seven men wearing protective clothing and exercising in hot-dry and hot-wet environmental conditions was applied to test the validity of the present index. PSI differentiated significantly ( P < 0.05) between the two climates. This index has the potential to be widely accepted and to serve universally after extending its validity to women and other age groups.
Integrating stimulus responsive materials and microfluidics: The key to next-generation chemical sensors

New generations of chemical sensors require both innovative (evolutionary) engineering concepts and (revolutionary) breakthroughs in the fundamental materials chemistry, such as the emergence of new types of stimuli responsive materials. In recent years, intensive research in those fields has brought interesting new concepts and designs for microfluidic flow control and sample handling that integrate high-quality engineering with new materials. In this article, we review the recent developments in this fascinating area of science, with particular emphasis on photoswitchable soft actuators and their incorporation into fluidic devices that are increasingly biomimetic in nature.