Miracle-dz/UniFAR-FTUs huggingface dataset:
Miniproteins as Phage Display-Scaffolds for Clinical Applications

Miniproteins are currently developed as alternative, non-immunoglobin proteins for the generation of novel binding motifs. Miniproteins are rigid scaffolds that are stabilised by alpha-helices, beta-sheets and disulfide-constrained secondary structural elements. They are tolerant to multiple amino acid substitutions, which allow for the integration of a randomised affinity function into the stably folded framework. These properties classify miniprotein scaffolds as promising tools for lead structure generation using phage display technologies. Owing to their high enzymatic resistance and structural stability, miniproteins are ideal templates to display binding epitopes for medical applications in vivo. This review summarises the characteristics and the engineering of miniproteins as a novel class of scaffolds to generate of alternative binding agents using phage display screening. Moreover, recent developments for therapeutic and especially diagnostic applications of miniproteins are reviewed.
Topological Generators and Cut-Graphs of Arbitrary Triangle Meshes

Recent advances in the parameterization and adaptive sampling of disc-like surfaces have brought a renewed interest on the global parameterization problem and, more specifically, on the cut-graph search. This paper focuses on the calculation of a family of generators and cut-graphs for the global parameterization of arbitrary triangle meshes. This result is achieved by combining the construction of harmonic scalar fields f : M rarr R of known maxima and minima with the quasi Morse-Smale complex of(M, f). The proposed technique has a simple implementation and outperforms previous work in terms of smoothness of the cut-graphs, stability with respect to the surface sampling, tessellation, topological noise (e.g., tiny handles), and capability of handling boundary components. Since we generate a family of cut-graphs, we also provide a comparison between the parameterizations of M induced by two cut-graphs.
On-line shear and extensional rheometry of polymer melts in the extrusion process

ON-LINE SHEAR AND EXTENSIONAL RHEOMETRY OF POLYMER MELTS IN THE EXTRUSION PROCESS Adrian Lee KELLY A novel on-line capillary rheometer (OLR) was used to examine the shear and extensional characteristics of polyolefin melts during twin screw extrusion (TSE). Comparisons with off-line rheometry were made using a twin-bore capillary rheometer and a modular in-line slit die rheorneter (ILR) provided in-line rheornetry comparisons. Both capillary rheometers were controlled via PCs running dedicated software, and the extrusion line and ELR were fully instrumented, allowing real-time process monitoring to be carried out by IBM compatible PCs via data acquisition hardware and software. Ihe prototype OLR was developed by the re-design of several key features including an instrumented transfer section and capillary die block which facilitated the use of various die geometries. Shear and extensional on-line rheometry of three polyethylenes (linear and branched), and four molecular weight grades of polypropylene were examined, and a direct comparison with off-line capillary rheometry showed a good correlation. Tle effect of a high loading of filler on two of the polyethylenes was investigated. In-line shear stress and entry pressure measurements showed a reasonable correlation with on-line rheornetry. A study of entry flows in the OLR using capillary dies approaching orifice showed non-linearities occurred at very low capillary length to diameter (L: D) ratios, and this was repeatable using off-line rheometry. Predicted zero length entry pressures (Po) were used to estimate apparent extensional viscosity using a number of standard models. Melt instability and capillary wall slip were also investigated using on-line rheometry. Melt pressure and temperature in the twin screw extruder and OLR were monitored at various process conditions to examine the ability of the OLR to condition melt during testing, and the effect of OLR testing on extrusion conditions. Pressure variation in the extruder, OLR and off-line rheometer were compared in order to quantify process noise. Tbe effect of OLR testing on melt rheology and polymer molecular weight were examined using off-line rheometry and gel permeation chromatography (GPQ.
Protocol-Independent Adaptive Replay of Application Dialog

For many applications—including recognizing malware variants, determining the range of system versions vulnerable to a given attack, testing defense mechanisms, and filtering multi-step attacks—it can be highly useful to mimic an existing system while interacting with a live host on the network. We present RolePlayer, a system which, given examples of an application session, can mimic both the client side and the server side of the session for a wide variety of application protocols. A key property of RolePlayer is that it operates in an application-independent fashion: the system does not require any specifics about the particular application it mimics. It instead uses byte-stream alignment algorithms to compare different instances of a session to determine which fields it must change to successfully replay one side of the session. Drawing only on knowledge of a few low-level syntactic conventions (such as representing IP addresses using “dotted quads”), and contextual information such as the domain names of the participating hosts, RolePlayer can heuristically detect and adjust network addresses, ports, cookies, and length fields embedded within the session, including sessions that span multiple, concurrent connections on dynamically assigned ports. We have successfully used RolePlayer to replay both the client and server sides for a variety of network applications, including NFS, FTP, and CIFS/SMB file transfers, as well as the multi-stage infection processes of the Blaster and
Virtual sensor: application to vehicle sideslip angle and transversal forces

This paper compares four observers (virtual sensors) of vehicle sideslip angle and lateral forces. The first is linear and uses a linear vehicle model. The remaining observers use an extended nonlinear model. The three nonlinear observers are: extended Luenberger observer, extended Kalman filter and sliding-mode observer. Modeling, model simplification, and observers are described, and an observability analysis is performed for the entire vehicle trajectory. The paper also deals with three different sets of sensors to see the impact of observers results. Comparison is first done by simulation on a valid vehicle simulator, and then observers are used on experimental data. Our study shows that observers are more accurate than simple models as regards unmeasurable variables such as sideslip angle and transversal forces. It also shows that speed of center of gravity is not an indispensable variable here.
Action potentials in the rat chromaffin cell and effects of acetylcholine.

1. Electrophysiological properties of the rat chromaffin cell were studied using intracellular recording techniques. 2. The resting potential in the chromaffin cell was ‐49 +/‐ 6 mV (mean +/‐ S.D., n = 14) in standard saline containing 10 mM‐Ca whereas that in Na‐free saline was ‐63 +/‐ 9 mV (n = 17). At rest, the membrane has a substantial Na permeability. 3. Action potentials were evoked by passing current through the recording electrode. In standard saline the major fraction of the action potential disappeared either upon omission of external Na ions from standard saline or addition of 1 muM tetrodotoxin (TTX). We conclude that action potentials in the chromaffin cell are due mainly to an increase in the permeability of the membrane to Na ions. 4. Small but significant regenerative action potentials were observed in Na‐free saline, and when Ca in Na‐free saline was replaced by Ba, prolonged action potentials occurred. We conclude that action potentials in the chromaffin cell also have a Ca component. 5. Iontophoretic application of acetylcholine (ACh) produced a transient membrane depolarization in standard saline. 6. Spontaneous action potentials were recorded extracellularly by microsuction electrodes. They occurred at a rate of 0‐05‐0‐1/sec in almost all cells. 7. When the perfusion fluid contained 3 x 10(‐7) M to 10(‐4) M ACh the spike frequency increased up to about 2/sec. This stimulatory effect of ACh was blocked by 10(‐7) M atropine but not by 10(‐3) M hexamethonium nor by 10(‐5) M‐d‐tubocurarine. 8. The importance of Ca entry during action potentials for catecholamine secretion is discussed
Towards Competence in Autonomous Agents

My thesis aims to contribute towards building autonomous agents that are able to develop what White (1959) called competency over their environment—agents that are able to achieve mastery over their domain and are able to solve new problems as they arise using the knowledge and skills they acquired in the past. While the field of machine learning has made much progress in solving individual, isolated problems, progress has been slow in developing agents that are able to interact effectively with their environment and flexibly deal with new tasks. There is still a large gap between the abilities of humans in this respect and the current capabilities of autonomous agents. My thesis will propose a number of methods for building competence in autonomous agents using the reinforcement learning (RL) framework, a computational approach to learning from interaction that has proved effective in certain types of problems (Sutton & Barto 1998). I expect that the methods I propose will extend the capabilities of RL agents in ways that are more than incremental, essentially allowing an autonomous agent to operate at a qualitatively different level.
Current Status of Developmental Immunotoxicity

Developmental immunotoxicity (DIT) occurs when exposure to environmental risk factors prior to adulthood, including chemical, biological, physical, or physiological factors, alters immune system development. DIT may elicit suppression, hyperactivation, or misregulation of immune responses and therefore may present clinically as decreased resistance to pathogens, allergic and autoimmune diseases, and inflammatory diseases. When evaluating DIT in an animal model, specific endpoints are assessed, which can reveal the potential for a risk factor to alter immune system development. However, linking DIT evaluation in an animal model with clinical realities observed in human populations requires that DIT testing regimens evaluate critical windows in immune system development. In addition, pathways leading to DIT may not be apparent without the stressors that induce aberrant and detectable responses. This review contains brief descriptions of recently published work that addresses disease patterns associated with DIT and solutions for altering such patterns of disease. We also comment on gaps between DIT testing in animal models and the clinical manifestation of immune-based diseases in children that can be filled by a better understanding of critical windows in immune system development and DIT testing that includes multiple functional assays.
Long-term Outcomes of a Postbaccalaureate Nurse Residency Program: A Pilot Study

OBJECTIVE: The purpose of this pilot study was to determine what influence a nurse residency program (NRP) has on long-term outcomes including turnover rates, career satisfaction, and leadership development. BACKGROUND: Studies examining short-term outcomes of NRPs have shown positive effects. Long-term studies of NRPs have not been reported. METHODS: This descriptive study surveyed former nurse residents, still employed at the facility. Data were collected by means of a demographic tool and the McCloskey/Mueller Satisfaction Scale, a job satisfaction tool. RESULTS: Although nursing turnover increased past the yearlong residency program, it remained well below the national average. All components of satisfaction were ranked relatively high, but coworker/peer support was most important to job satisfaction. Leadership development in the areas of certification and pursuing an advanced degree increased with longer employment, but hospital committee involvement decreased with successive cohorts. CONCLUSION: Overall, the long-term outcomes of an NRP appear to have benefits to both the organization and the individual.
Ultrasonic Sensing of Plant Water Needs for Agriculture

Fresh water is a key natural resource for food production, sanitation and industrial uses and has a high environmental value. The largest water use worldwide (~70%) corresponds to irrigation in agriculture, where use of water is becoming essential to maintain productivity. Efficient irrigation control largely depends on having access to reliable information about the actual plant water needs. Therefore, fast, portable and non-invasive sensing techniques able to measure water requirements directly on the plant are essential to face the huge challenge posed by the extensive water use in agriculture, the increasing water shortage and the impact of climate change. Non-contact resonant ultrasonic spectroscopy (NC-RUS) in the frequency range 0.1–1.2 MHz has revealed as an efficient and powerful non-destructive, non-invasive and in vivo sensing technique for leaves of different plant species. In particular, NC-RUS allows determining surface mass, thickness and elastic modulus of the leaves. Hence, valuable information can be obtained about water content and turgor pressure. This work analyzes and reviews the main requirements for sensors, electronics, signal processing and data analysis in order to develop a fast, portable, robust and non-invasive NC-RUS system to monitor variations in leaves water content or turgor pressure. A sensing prototype is proposed, described and, as application example, used to study two different species: Vitis vinifera and Coffea arabica, whose leaves present thickness resonances in two different frequency bands (400–900 kHz and 200–400 kHz, respectively), These species are representative of two different climates and are related to two high-added value agricultural products where efficient irrigation management can be critical. Moreover, the technique can also be applied to other species and similar results can be obtained.
Using Wikipedia categories for compact representations of chemical documents

Today, Web pages are usually accessed using text search engines, whereas documents stored in the deep Web are accessed through domain-specific Web portals. These portals rely on external knowledge bases, respectively ontologies, mapping documents to more general concepts allowing for suitable classifications and navigational browsing. Since automatically generated ontologies are still not satisfactory for advanced information retrieval tasks, most portals heavily rely on hand-crafted domain-specific ontologies. This, however, also leads to high creation and maintaining costs. On the other hand, a freely available community maintained, if somewhat general, knowledge base is offered by Wikipedia. During the last years the coverage of Wikipedia has reached a large pool of information including articles from almost all domains. In this paper, we investigate the use of Wikipedia categories to describe the content of chemical documents in a compact form. We compare the results to the domain-specific ChEBI ontology and the results show that Wikipedia categories indeed allow useful descriptions for chemical documents that are even better than descriptions from the ChEBI ontology.
Does it Matter What They Said? A Text Mining Analysis of the State of the Union Addresses of USA Presidents

Text data are a major type of data in the modern society. Literatures have pointed out that more than 80% of data are in text form. It is important to study the insights from text data in addition to quantitative data. The development of text mining techniques started in the early 80's. The methodology has become much more mature in the recent years. In this article, we conduct a case study using text mining technique to analyze the patterns of the president's State of the Union address in USA. The speeches analyzed include the recent four USA presidents, Bush (1989-1992), Clinton (1993 - 2000), G.W. Bush (2001-2008), and Obama (2009-2011). Using two different text mining techniques, we identify six clusters from the 23 speeches using one technique and obtain seven topics based on the other technique.
Sales, Inventories, and Real Interest Rates: A Century of Stylized Facts

We use Bayesian time-varying parameters structural VARs with stochastic volatility to investigate changes in both the reduced-form and the structural correlations between business inventories and either sales growth or the real interest rate in the United States during both the interwar and the post-WWII periods. We identify four structural shocks by combining a single long-run restriction to identify a permanent output shock as in Blanchard and Quah (1989), with three sign restrictions to identify demand- and supply-side transitory shocks. We produce several new stylized facts which should inform the development of new models of inventories. In particular, we show that (i) during both the interwar and the post-WWII periods, the structural correlation between inventories and the real interest rate conditional on identified interest rate shocks is systematically positive; (ii) the reduced-form correlation between the two series is positive during the post-WWII period, but in line with the predictions of theory it is robustly negative during the interwar era; and (iii) during the interwar era, the correlations between inventories and either of the two other series exhibits a remarkably strong co-movement with output at the business-cycle frequencies.
Further Improvement in Postprandial Glucose Control With Addition of Exenatide or Sitagliptin to Combination Therapy With Insulin Glargine and Metformin

OBJECTIVE To assess the effect of a 4-week adjunctive therapy of exenatide (EXE) (5–10 μg b.i.d.) or sitagliptin (SITA) (100 mg once daily) in response to a standardized breakfast meal challenge in 48 men or women with type 2 diabetes receiving insulin glargine (GLAR) + metformin (MET). RESEARCH DESIGN AND METHODS This was a single-center, randomized, open-label, active comparator–controlled study with a three-arm parallel group design, consisting of: screening, 4- to 8-week run-in period, 4-week treatment period, and follow-up. In all three groups, the GLAR dose was titrated according to an algorithm (fasting blood glucose ≤100 mg/dl). RESULTS The unadjusted 6-h postprandial blood glucose excursion of both GLAR + MET + EXE and GLAR + MET + SITA was statistically significantly smaller than that of GLAR + MET (606 ± 104 vs. 612 ± 133 vs. 728 ± 132 mg/dl/h; P = 0.0036 and 0.0008). A1C significantly decreased in all three groups (P < 0.0001), with the greatest reduction of −1.9 ± 0.7 under GLAR + MET + EXE (GLAR + MET + SITA −1.5 ± 0.7; GLAR + MET −1.2 ± 0.5%-points; GLAR + MET + EXE vs. GLAR + MET P = 0.0154). The American Diabetes Association A1C target of <7.0% was reached by 80.0, 87.5, and 62.5% of subjects, respectively. GLAR + MET + EXE had the highest number (47) of adverse events, mostly gastrointestinal (56%) with one dropout. GLAR + MET or GLAR + MET + SITA only had 10 and 12 adverse events, respectively, and no dropouts. Hypoglycemia (blood glucose <50 mg/dl) rates were low and comparable among groups. Weight decreased with GLAR + MET + EXE (−0.9 ± 1.7 kg; P = 0.0396) and increased slightly with GLAR + MET (0.4 ± 1.5 kg; NS; GLAR + MET + EXE vs. GLAR + MET P = 0.0377). CONCLUSIONS EXE or SITA added to GLAR + MET further substantially reduced postprandial blood glucose excursions. Longer-term studies in a larger population are warranted to confirm these findings.
What Makes an Effective Teacher? Quasi-Experimental Evidence

I estimate in this article the effect of teaching practices on student achievements. I find that teaching based on the instilment of knowledge and comprehension (‘traditional’ teaching), and techniques that endow pupils with analytical and critical skills (‘modern’ teaching) has strong positive effect on test scores. However, a second element of modern teaching, instilment of the capacity for individual study has no effect while transparency, fairness, and feedback in teachers’ conduct with their students improve marginally academic performance. Heterogeneity in these effects suggests that it is best to target the two teaching practices differentially to students of different genders and abilities.
Hands-Off Control as Green Control

In this article, we introduce a new paradigm of control, called hands-off control, which can save energy and reduce CO2 emissions in control systems. A hands-off control is defined as a control that has a much shorter support than the horizon length. The maximum hands-off control is the minimum support (or sparsest) control among all admissible controls. With maximum hands-off control, actuators in the feedback control system can be stopped during time intervals over which the control values are zero. We show the maximum hands-off control is given by L1 optimal control, for which we also show numerical computation formulas.
Transforming Growth Factor-β1 as a Common Target Molecule for Development of Cardiovascular Diseases, Renal Insufficiency and Metabolic Syndrome

Transforming growth factor-β1 (TGF-β1) is a polypeptide member of the transforming growth factor β superfamily of cytokines. It is a secreted protein that performs many cellular functions including control of cell growth, cell proliferation, cell differentiation and apoptosis. In the cardiovascular system, TGF-β1 plays pivotal roles in the pathogenesis of hypertension, restenosis after percutaneous coronary intervention, atherosclerosis, cardiac hypertrophy and heart failure. In addition, TGF-β1 has been shown to be increased in adipose tissue of obese subjects with insulin resistance. Furthermore, TGF-β1 is a potent initiator of proliferation of renal mesangial cells leading to chronic kidney disease. Some currently available agents can manipulate TGF-β1 expression leading to amelioration of cardiovascular diseases. Thus, an understanding of interactions between chronic kidney disease and metabolic syndrome and the development of cardiovascular diseases is an important issue, and attention should be given to TGF-β1 as a crucial factor for regulation and modulation of those pathological conditions.
Representation Learning of Music Using Artist Labels

Recently, feature representation by learning algorithms has drawn great attention. In the music domain, it is either unsupervised or supervised by semantic labels such as music genre. However, finding discriminative features in an unsupervised way is challenging, and supervised feature learning using semantic labels may involve noisy or expensive annotation. In this paper, we present a feature learning approach that utilizes artist labels attached in every single music track as an objective meta data. To this end, we train a deep convolutional neural network to classify audio tracks into a large number of artists. We regard it as a general feature extractor and apply it to artist recognition, genre classification and music auto-tagging in transfer learning settings. The results show that the proposed approach outperforms or is comparable to previous state-of-the-art methods, indicating that the proposed approach effectively captures general music audio features.