Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and Evaluation of Methods for Predicting Protein Levels and Peak Intensities from Tandem Mass Spectrometry Data

Tandem mass spectrometry (MS/MS) of peptides is a central technology for proteomics, enabling the identification of thousands of proteins and peptides from a complex mixture. With the increasing acquisition rate of tandem mass spectrometers, it has become possible to use data-mining techniques to attempt to solve important biological problems using MS/MS data. These problems include (i) estimating the levels of the thousands of proteins in a tissue sample, (ii) predicting the intensity of the peaks in a mass spectrum, and (iii) explaining why different peptides from the same protein have different peak intensities. In this paper, we develop and evaluate several simple data-mining techniques for tackling these biological problems. The main data-mining problem is to untangle the various factors that affect the intensity of a peak in a mass spectrum. To this end, we develop three statistical models of MS/MS data: linear, exponentiated linear, and inverse linear. For each model, we develop a family of methods for fitting the model to the data. We test each method on both simulated and real-world data, where the real data consists of three datasets generated by MS/MS experiments performed on various tissue samples taken from Mouse. Because of the highly skewed distribution of the data, which also ranges over several orders of magnitude, we measure the fit of each model to the data using Spearman’s rank correlation coefficient, instead of the more common Pearson correlation coefficient. Finally, we compare the methods to a number of naive methods, and report on their performance. keywords: Proteomics, Data Mining, Machine Learning, Peptide Tandem Mass Spectrometry.
Understanding the Role of Sender Reputation in Abuse Reporting and Cleanup

Motivation: Participants on the front lines of abuse reporting have a variety of options to notify intermediaries and resource owners about abuse of their systems and services. These can include emails to personal messages to blacklists to machine-generated feeds. Recipients of these reports have to voluntarily act on this information. We know remarkably little about the factors that drive higher response rates to abuse reports. One such factor is the reputation of the sender. In this article, we present the first randomized controlled experiment into sender reputation. We used a private datafeed of Asprox-infected websites to issue notifications from three senders with different reputations: an individual, a university and an established anti-malware organization. Results: We find that our detailed abuse reports significantly increase cleanup rates. Surprisingly, we find no evidence that sender reputation improves cleanup. We do see that the evasiveness of the attacker in hiding compromise can substantially hamper cleanup efforts. Furthermore, we find that the minority of hosting providers who viewed our cleanup advice webpage were much more likely to remediate infections than those who did not, but that website owners who viewed the advice fared no better.
The relationship between the prescription of pyschotropic drugs and suicide rates in adults in England and Wales

Background A few studies have demonstrated an inverse relationship between the general population and suicide rates and antidepressant prescribing rates. Correlations between general population suicide rates and prescribing rates of other psychotropic drugs have also been observed. There have not been any studies during the last decade. Methods The relationship between adult suicide rates and prescription rates of psychotropic drugs by the broad British National Formulary (BNF) categories, for individual psychotropic drug groups within the BNF categories (e.g. selective serotonin reuptake inhibitors) and for individual psychotropic drugs was examined over a 12-year period (1995–2006) was examined using Spearman’s rank correlation. All data were ascertained from the archives of the Office for National Statistics. Results There was an absence of significant correlations between adult suicides rates and rates of prescriptions of psychotropic drugs in the broad BNF categories, individual psychotropic drug groups and individual psychotropic drugs. Discussion The findings may be due to methodological errors. Should the findings be accurate, then the following approaches require consideration to reduce suicide rates further: (i) development of strategies to ensure continued prescription of psychotropic drugs at the current level; (ii) development of strategies to improve non-pharmacological measures, including improved mental health services provision for adults, improved assessment of suicide risk, increased availability of psychosocial interventions and restricting the availability of methods of suicide; and (iii) development of strategies to implement improvement in distal risk (e.g. societal socio-economic status) and protective (e.g. societal educational attainment) factors for suicide at a societal level.
BIMEL, an intrinsically disordered protein, is degraded by 20S proteasomes in the absence of poly-ubiquitylation

BIM-extra long (BIMEL), a pro-apoptotic BH3-only protein and part of the BCL-2 family, is degraded by the proteasome following activation of the ERK1/2 signalling pathway. Although studies have demonstrated poly-ubiquitylation of BIMEL in cells, the nature of the ubiquitin chain linkage has not been defined. Using ubiquitin-binding domains (UBDs) specific for defined ubiquitin chain linkages, we show that BIMEL undergoes K48-linked poly-ubiquitylation at either of two lysine residues. Surprisingly, BIMELΔKK, which lacks both lysine residues, was not poly-ubiquitylated but still underwent ERK1/2-driven, proteasome-dependent turnover. BIM has been proposed to be an intrinsically disordered protein (IDP) and some IDPs can be degraded by uncapped 20S proteasomes in the absence of poly-ubiquitylation. We show that BIMEL is degraded by isolated 20S proteasomes but that this is prevented when BIMEL is bound to its pro-survival target protein MCL-1. Furthermore, knockdown of the proteasome cap component Rpn2 does not prevent BIMEL turnover in cells, and inhibition of the E3 ubiquitin ligase β-TrCP, which catalyses poly-Ub of BIMEL, causes Cdc25A accumulation but does not inhibit BIMEL turnover. These results provide new insights into the regulation of BIMEL by defining a novel ubiquitin-independent pathway for the proteasome-dependent destruction of this highly toxic protein.
Incremental placement for timing optimization

An incremental timing driven placement algorithm is presented. We introduce a fast path-based analytical approach for timing improvement. Our method achieves timing optimization by reducing the enclosing bounding boxes of selected nets on critical paths. Furthermore, this technique tries to minimize modifications to the initial placement while improving the delay of the circuit incrementally. Two contributions of this work are 1) efficient conversion of a path-based timing minimization problem to a geometric net-constraint problem and 2) minimal modification of a placement to improve timing. Our technique can take an initial placement from any algorithm and improve timing iteratively. The experiments show that the proposed approach is very efficient.
Vitamin E Reduction of Protein Glycosylation in Diabetes: New Prospect for Prevention of Diabetic Complications?

Objective This study evaluated the possibility of inhibiting protein glycosylation in vivo with vitamin E. Research Design and Methods Two groups of 10 insulin-requiring diabetic patients, matched for duration of disease and metabolic control, received daily vitamin E supplementation of 1200 and 600 mg, respectively, for 2 mo. A third group of 10 diabetic patients, matched for duration of disease and metabolic control, served as the control group and received placebo. Fasting plasma glucose, mean daily plasma glucose, fasting labile HbA1, and glycosylated proteins were measured in the basal state and after 1 and 2 mo of treatment. In addition, hyperglycemic clamp studies were performed in basal state and after 1 mo of vitamin E administration in all patients. Results Glycemic indices did not show any significant changes during the study, whereas fasting labile HbA, and glycosylated proteins decreased significantly after 1 and 2 mo in patients on vitamin E administration. Stable HbA1 decreased after 2 mo. Mean glycemic incremental area in the hyperglycemic clamp procedure was similar before and after treatment, whereas a significant reduction in mean labile HbA1 incremental area was found after vitamin E supplementation. A significant difference was also found in both fasting and incremental labile HbA1 levels, stable HbA1, and glycosylated proteins between the two groups of diabetic patients on the two doses of vitamin E; the diabetic patients who received the higher dose of vitamin E showed the greater reduction. No significant changes in these parameters were observed in diabetic patients on placebo administration. Conclusions These results demonstrate that vitamin E administration may reduce protein glycosylation in diabetic subjects independently of changes in plasma glucose, an effect that may be due to the inhibition of labile glycosylation, the first step of the Maillard reaction. Long-term studies will help establish the usefulness of vitamin E administration for the prevention of diabetic complications.
Doped Nanocrystals

The critical role that dopants play in semiconductor devices has stimulated research on the properties and the potential applications of semiconductor nanocrystals, or colloidal quantum dots, doped with intentional impurities. We review advances in the chemical synthesis of doped nanocrystals, in the theoretical understanding of the fundamental mechanisms that control doping, and in the creation of highly conducting nanocrystalline films. Because impurities can be used to alter the properties of nanoscale materials in desirable and controllable ways, doped nanocrystals can address key problems in applications from solar cells to bioimaging.
Adiponectin is associated with vascular function independent of insulin sensitivity.

OBJECTIVE Adiponectin has been proposed to play important roles in the regulation of energy homeostasis and insulin sensitivity. In experimental studies, adiponectin has also been found to inhibit vascular smooth muscle cell proliferation. Decreased adiponectin levels have been described in patients with coronary artery disease, and circulating adiponectin predicts cardiovascular death in patients with renal failure. Because adiponectin appears to influence both insulin sensitivity and vessel wall physiology, we examined insulin sensitivity and vascular function in relation with circulating adiponectin. RESEARCH DESIGN AND METHODS We studied brachial artery vascular reactivity (high-resolution external ultrasound) and insulin sensitivity (minimal model) in 68 healthy subjects. Brachial artery vascular reactivity was also determined in 52 patients with altered glucose tolerance: 30 subjects with impaired fasting glucose (IFG) or glucose intolerance (GIT) and 22 patients with type 2 diabetes. RESULTS Circulating adiponectin concentration was significantly associated with insulin sensitivity (r=0.29, P=0.02) and with fasting serum triglycerides (r=-0.29, P=0.02) in healthy subjects. In the latter, adiponectin levels were positively associated with arterial vasodilation in response to nitroglycerin (endothelium-independent vasodilation [EIVD], r=0.41, P=0.002) but not with flux-induced, endothelium-dependent vasodilation (EDVD) (r=0.007, P=NS). In contrast, EIVD was not significantly associated with adiponectin in subjects with IFG, GIT, or type 2 diabetes (r < or =0.10, P=NS). In a multiple linear regression analysis to predict EIVD in healthy subjects, age (P=0.012), sex (P=0.042), and adiponectin concentration (P=0.045), but not BMI, insulin sensitivity, or fasting triglycerides, contributed to 39% of EIVD variance. CONCLUSIONS Serum adiponectin concentration appears to be significantly associated with vascular function in apparently healthy humans. This association seems to be independent of its link with insulin sensitivity.
Decision support tool for group job-shop scheduling problems

This paper presents a new tool for group job-shop scheduling problems. The tool encompasses a dynamic Pareto-optimal method based on two criteria simultaneously: relative setup expenditure criterion and average orders utility criterion. In this method the concept of production intensity as a dynamic production process parameter is used. The software used allows scheduling for medium quantity of jobs. The result of software application is the set of non-dominant versions proposed to a user for making a final choice. Based on this model, a decision support tool (DST) called OptJobShop is used for scheduling optimization. The decision support tool provides for scheduling simulation with various initial parameters, comparison of different scheduling versions and choice of the final decision.
Implementation of Low Leakage and High Performance 8-Bit ALU for Low Power Digital Circuits

The insist for portable devices is fulfilled by the growing CMOS technology. As the size of the transistor shrinks, the leakage power component augments exponentially. Thus it becomes a critical metric for the future technologies. This paper deals with the techniques like GATED VDD, AVLS, AVLG, and AVL for reducing leakage power. These techniques are implemented on 8-bit ALU. 80% of cutback in leakage power can be achieved by applying proposed technique with minimum delay and area overhead. The circuit is simulated on cadence(R) Virtuoso(R) in 90 nanometer CMOS technology.
Studies of Electrical and Thermal Conductivities of Sheared Multi-Walled Carbon Nanotube with Isotactic Polypropylene Polymer Composites

Polymer nanocomposite materials of higher thermal and electrical transport properties are important to nanotechnology applications such as thermal management, packaging, labelling and the textile industry. In this work, thermal and electrical conductivities in nanocomposites of multiwalled carbon nanotubes (MWCNT) and isotactic polypropylene (iPP) are investigated in terms of MWCNT loading, temperature dependence, and anisotropy caused by melt shearing. IPP/MWCNT nanocomposites show a significant increase in thermal and electrical conductivity with increasing MWCNT loading, reaching 17.5 W/m K and 10−6 S/m, respectively, at a MWCNT 5.0 weight percentage at 40°C. The increase in MWCNT/iPP is more than would be expected based on the additivity rule, and suggests a reduction of the interfacial thermal electrical resistance at nanotube-nanotube junctions and the nanotube-matrix interface. The anisotropy in both conductivities was observed to be larger at low temperature and to disappear at higher temperature due to isotropic electrical and thermal contact in both directions. Oriented MWCNT/iPP nanocomposites exhibit higher electrical and thermal conductivities, attributed primarily by orientation of nanotubes due to the shearing fabrication process.
Indications for Catheter-Directed Thrombolysis in the Management of Acute Proximal Deep Venous Thrombosis

Deep vein thromboses (DVTs) cause significant morbidity and mortality in the general population. Oral anticoagulation therapy may reduce thrombus propagation but does not cause clot lysis and therefore does not prevent postthrombotic syndrome (PTS). Catheter-directed thrombolysis (CDT) can be used to treat DVTs as an adjunct to medical therapy, but there is no consensus defining exact indications. Current evidence suggests that CDT can reduce clot burden and DVT recurrence and consequently prevents the formation of PTS compared with systemic anticoagulation. Appropriate indications include younger individuals with acute proximal thromboses, a long life expectancy, and relatively few comorbidities. Limb-threatening thromboses may also be treated with CDT, although the subsequent mortality remains high. A number of randomized controlled trials are currently under way comparing the longer-term outcomes of CDT compared with anticoagulation alone. Initial reports suggest that venous patency and valvular function are better maintained after CDT. The effectiveness of combined pharmacomechanical thrombectomy and the role of vena cava filters need to be investigated further before strong recommendations can be made. The reported short-term outcomes following catheter-based intervention for DVT are encouraging in selected patients. Further evidence is required to establish long-term benefits and cost-effectiveness.
A detailed path-latency model for router geolocation

This study outlines two novel techniques which can be used in the area of IP geolocation. First we introduce a detailed path-latency model to be able to determine the overall propagation delays along the network paths more accurately. This knowledge then leads to more precise geographic distance estimation between network routers and measurement nodes. In addition to the application of the detailed path-latency model, we describe a method which utilizes high-precision one-way delay measurements to further increase the accuracy of router geolocation techniques. The precise one-way delay values are used as a “path-constraint” to limit the overall geographic distance between the measurement nodes. The approach introduced in this paper can be used to localize all the network routers along the network path between the measurement nodes and can be combined with other existing geolocation techniques. The introduced techniques are validated in a wide range of experiments performed in the ETOMIC measurement infrastructure.
Sparse Coding of Point Cloud Data

Point clouds, made available through laser range finders, stereo cameras, or time of flight cameras, are frequently used in robot navigation systems. However, no unsupervised machine perception algorithm exists to provide understanding of the data; e.g. that a particular blob of points looks roughly like, say, a car. In this paper, we take steps towards such an algorithm based on sparse coding. The work here generalizes to any binary data. An algorithm for learning the bases and the activations for point cloud data is derived and demonstrated. Given precomputed basis vectors and an input vector, calculating the activations is very fast and could be used in real-time applications.
THEORY AND MEASUREMENT OF VISUAL MECHANISMS

The several parameters of the flicker response contour (F – log I) are considered as a function of wave-length composition (white, blue, and red) and light-time fraction, for an extra-foveal region (monocular, temporal retina). These data are compared with those secured for the same image area centrally fixated at the fovea. The systematic changes in the parameters are shown to be in rational relation to other relevant excitability data. Since for two retinal regions the primary contours are quite different, the systematic nature of the behavior of the parameters in the two cases is a real test of the power of the analysis proposed. Theoretical interpretation is required to deal with the properties of sets of performance contours under systematically varied conditions, and cannot rely simply on the comparison of (for example) two contours under the same arbitrary conditions at two retinal locations. In particular it is emphasized that a qualitative separation must be made of the two factors of (a) number of units and (b) the frequencies of their actions, before the wave-length problem can be dealt with effectively.
Context-aware integrated development environment command recommender systems

Integrated development environments (IDEs) are complex applications that integrate multiple tools for creating and manipulating software project artifacts. To improve users' knowledge and the effectiveness of usage of the available functionality, the inclusion of recommender systems into IDEs has been proposed. We present a novel IDE command recommendation algorithm that, by taking into account the contexts in which a developer works and in which different commands are usually executed, is able to provide relevant recommendations. We performed an empirical comparison of the proposed algorithm with state-of-the-art IDE command recommenders on a real-world data set. The algorithms were evaluated in terms of precision, recall, F1, k-tail, and with a new evaluation metric that is specifically measuring the usefulness of contextual recommendations. The experiments revealed that in terms of the contextual relevance and usefulness of recommendations the proposed algorithm outperforms existing algorithms.
A Structural Analysis of SLAs and Dependencies Using Conceptual Modelling Approach

Making good use of Service Level Agreements (SLA) becomes crucial for an enterprise both to provide value added products and services to customers and to protect the interest of parties involved in the business activities. Well formed and effective structural representation and management of SLAs in conceptual modeling can greatly support the understanding and communication of service development and deployment as well as maintenance of quality of service. Existing specifications and structures for SLAs do not fully formalize and support for different automatic and dynamic behavioral aspects needed within business enterprises due to lack of study focusing on SLAs templates and their contents, which are mostly written on Natural Language (NL). We address the issues of how to use conceptual models to describe the structures of SLAs and the various relationships between SLAs and their items, and hence to better depict business domains. With focus on the contents, process, and dependencies among SLAs, we aim to use so generated concept model for service discovery, service delivery and scheduling.
The Known Unknowns of the Human Dendritic Cell Network

Dendritic cells (DCs) initiate and orient immune responses and comprise several subsets that display distinct phenotypes and properties. Most of our knowledge of DC subsets biology is based on mouse studies. In the past few years, the alignment of the human DC network with the mouse DC network has been the focus of much attention. Although comparative phenotypic and transcriptomic analysis have shown a high level of homology between mouse and human DC subsets, significant differences in phenotype and function have also been evidenced. Here, we review recent advances in our understanding of the human DC network and discuss some remaining gaps and future challenges of the human DC field.