Miracle-dz/UniFAR-FTUs huggingface dataset:
A New Paradigm for Personalized Medicine and Companion Diagnostics: The Contract Diagnostics Organization

In the era of personalized medicine, pharmaceutical companies are actively seeking partners to develop Com- panion diagnostics. Common choices of partners include large diagnostic manufacturers and traditional Contract Research Organizations (CROs), neither of which provides an entire solution. Diagnostics companies have an intrinsic bias toward internal product lines, and are therefore incentivized to direct diagnostics development toward an existing technology plat- form. The expertise of a CRO lies in the monitoring of pharmaceutical programs, not in diagnostics. In addition, few tradi- tional partners have significant clinical laboratory experience or offer accredited clinical laboratories to ensure that the di- agnostic clinical trials are designed for, and conducted in, laboratories that meet regulatory standards. Lastly, these or- ganizations are inexperienced in managing and coordinating the multiple partners required in the development process. The Contract Diagnostics Organization (CDO) is a new concept designed to aid pharmaceutical companies in addressing challenges in companion diagnostics development. This business model provides pharmaceutical companies a complete outsourcing partner to initiate and manage the parallel development of companion diagnostic tests in synergy with drug development. The CDO combines all of the necessary services, including diagnostics research, an accredited clinical labo- ratory, project management and regulatory, manufacturing, and consulting in an integrated, technology-independent man- ner. Thus, the CDO focuses on its pharmaceutical partner's business objectives and ensures the speediest path to market a valuable, personalized drug for patients.
Boundary observer design for hyperbolic PDE in rotary drilling systems

It is well known that vibrations in oilwell system affect the drilling directions and may be inherent for drilling systems. Further, the environment complexity requires a minimum number of sensor variables. In this paper, for an oilwell drilling system, we present an adaptive observer design for a second-order Partial Differential Equation (PDE) with the usually neglected damping term. The design relies on the top boundary measurements only. From the Lyapunov theory and the backstepping technique, we develop an observer based control law for the one dimension wave PDE. We show an exponentially vibration stability of the partially equipped oilwell drilling system. The simulation results confirm the effectiveness of the proposed PDE observer based controller.
Gene Expression Profiling Reflects Physiological Processes in Salt Acclimation of Synechocystis sp. Strain PCC 68031

The kinetics of genome-wide responses of gene expression during the acclimation of cells of Synechocystis sp. PCC 6803 to salt stress were followed by DNA-microarray technique and compared to changes in main physiological parameters. During the first 30 min of salt stress, about 240 genes became induced higher than 3-fold, while about 140 genes were repressed. However, most changes in gene expression were only transient and observed among genes for hypothetical proteins. At 24 h after onset of salt stress conditions, the expression of only 39 genes remained significantly enhanced. Among them, many genes that encode proteins essential for salt acclimation were detected, while only a small number of genes for hypothetical proteins remained activated. Following the expression of genes for main functions of the cyanobacterial cell, i.e. PSI, PSII, phycobilisomes, and synthesis of compatible solutes, such as ion homeostasis, distinct kinetic patterns were found. While most of the genes for basal physiological functions were transiently repressed during the 1st h after the onset of salt stress, genes for proteins specifically related to salt acclimation were activated. This gene expression pattern reflects well the changes in main physiological processes in salt-stressed cells, i.e. transient inhibition of photosynthesis and pigment synthesis as well as immediate activation of synthesis of compatible solutes. The results clearly document that following the kinetics of genome-wide expression, profiling can be used to envisage physiological changes in the cyanobacterial cell after certain changes in growth conditions.
An Algorithm for Multi-Unit Combinatorial Auctions

We present a novel algorithm for computing the optimal winning bids in a combinatorial auction (CA), that is, an auction in which bidders bid for bundles of goods. All previously published algorithms are limited to single-unit CAs, already a hard computational problem. In contrast, here we address the more general problem in which each good may have multiple units, and each bid speci€es an unrestricted number of units desired from each good. We prove the correctness of our branch-and-bound algorithm, which incorporates a specialized dynamic programming procedure. We then provide very encouraging initial experimental results from an implemented version of the algorithm.
Applications of Hemagglutinating Virus of Japan in therapeutic delivery systems

Background: Efficient and minimally invasive vector systems appear to be the most appropriate for both gene therapy and drug delivery. Numerous viral and non-viral vectors have been developed. Each vector has its own advantages and limitations. Objective: New vectors have been required for overcoming the limitations of both viral vectors and non-viral vectors. The idea is to compensate the limitations of one vector system with the advantages of another. This can enable efficient drug delivery and gene expression, while reducing the cytotoxicity of the various vector components. Methods: The Hemagglutinating Virus of Japan (HVJ; Sendai virus) envelope vector was developed using fusion-competent inactivated HVJ particle. Briefly, the viral genome was destroyed by UV-irradiation, and the inactivated viral particles were mixed with plasmid DNA, proteins or siRNA in the presence of mild detergent. After centrifugation, those molecules were incorporated into the viral envelope. Conclusion: The HVJ-E vector can efficiently deliver therapeutic molecules such as genes, siRNA, decoy oligonucleotides, proteins, and anti-cancer drugs to various tissues in vivo. It is also available for high throughput screening of therapeutic genes. A number of anti-cancer effects of HVJ-E have been identified, specifically activation of both T cell immunity and non-T cell immunity against cancers. Furthermore, a tissue-targeting HVJ-E vector has been constructed using a unique approach for virus engineering and by conjugation with biocompatible polymers. Therefore, the HVJ-E vector is expected to enable effective cancer therapy through the delivery of molecular therapy and through its immunotherapeutic effects.
Puercolestes and Betonnia (Cimolestidae, Mammalia) from the early Paleocene (Puercan 3 Interval Zone) of northeastern Montana, U.S.A.

In northeastern Montana, fossil localities in the Garbani Channel Complex and other early Paleocene (Puercan 3 Interval Zone) localities are preserved in the Tullock Member of the Fort Union Formation. They document an early phase in the recovery of the terrestrial fauna of the North American Western Interior after the mass extinction marking the Cretaceous-Paleogene (K-Pg) boundary. The cimolestids Puercolestes simpsoni and Betonnia tsosia were typified on fragmentary jaws and isolated teeth found in Puercan 2 and 3 Interval Zones (Pu2, Pu3) in the Nacimiento Formation, San Juan Basin, New Mexico. The available samples of these genera from both New Mexico and Montana are small and dominantly consist of isolated teeth. Characters of upper cheek teeth, P4 and M1–M3, justify provisional recognition of Puercolestes sp. cf. Pu. simpsoni and the somewhat smaller Betonnia sp. cf. Be. tsosia in Pu3 local faunas in the Tullock Member. In contrast, discovery of characters distinguishing the isolated lower cheek teeth, p4s and m1–m3s, of these species must await recovery of dentulous dentaries documenting the patterns of morphological variation of their lower dentitions. Fossils from the Tullock Member add support to the current interpretation that cimolestids were taxonomically diverse and geographically widespread but relatively rare members of the faunas of the North American Western Interior during approximately the first million years of the Paleocene.
Vibration control of a flexible arm for the ITER maintenance using unknown visual features from inside the vessel

In this paper we present a vibration control scheme for a long-reach inspection arm in an environment as constrained as a fusion reactor. The ultra-high vacuum, the high operating temperature, the significant residual magnetic field and the nuclear activation in ITER will prevent from considering common on-the-shelf dynamics sensors. Therefore we propose to use the already developed rad-hardened viewing tool to feed an oscillation observer with visual information. In our approach the visual data are extracted from a totally unknown environment. Particular attention is paid to obtain a robust algorithm. Experimental results validate the proposed strategy.
The Influence of Interpersonal Relationships on Nurse Managers’ Work Engagement and Proactive Work Behavior

OBJECTIVE: This study tested the effects of interpersonal relationships on nurse managers’ work engagement and proactive work behavior. BACKGROUND: An engaged workforce may help healthcare organizations improve performance. In healthcare, nurse managers are responsible for creating motivating work environments. They also need to be engaged, yet little is known about what influences nurse managers’ performance. METHODS: A self-administered electronic survey was used to collect data from 323 nurse managers working in acute care hospitals. Instruments included the Relational Coordination Scale, Utrecht Work Engagement Scale, and Proactive Work Behavior Scale. RESULTS: Interpersonal relationships with nurse administrators were most predictive of nurse managers’ work engagement. Interpersonal relationships with physicians were most predictive of nurse managers’ proactive work behavior. CONCLUSION: Organizational cultures that foster quality interpersonal relationships will support the job performance of nurse managers.
Correlates of Stimulant Treatment Outcome Across Treatment Modalities

Objective: This study evaluated variables associated with stimulant use outcomes in stimulant users (N = 800) receiving care in community outpatient psychosocial or methadone maintenance treatment clinics as part of a national multi-site clinical trial. Methods: Results from the full sample were examined first, and then predictors were examined separately in the two treatment modalities. Results: A cocaine-positive urine sample at study intake was the most robust and consistent correlate of stimulant use outcome in all analyses. Psychiatric distress, social environment and employment had differential effects on outcome across modalities. Conclusions/Significance: This study confirms that intake assessments have considerable value in identifying problems to be addressed in treatment.
Study on the Effective Measures of Enhancing the Fractal Image Coding

The fractal image coding is an effective method of data compression and its prospects are bright for the future. But due to the high computation order of complexity difficulty it faces, it can't be applied widespreadly until now. The author of this article proposes a fast coding algorithm that could reduce the complexity of fractal code computation order and the time. The experimental results indicated that by this algorithm we can get the anticipated effect of fast realization fractal image encoding under the condition of not reducing the reconstruction image vision effect.
Determining Drivers for Wildebeest (Connochaetes taurinus) Distribution in the Masai Mara National Reserve and Surrounding Group Ranches

DETERMINING DRIVERS FOR WILDEBEEST (CONNOCHAETES TAURINUS) DISTRIBUTION IN THE MASAI MARA NATIONAL RESERVE AND SURROUNDING GROUP RANCHES by Meghan Marie Sheehan A current assessment of wildebeest (Connochaetes taurinus) distribution throughout the Masai Mara National Reserve (MMNR) and adjoining group ranches has not been investigated for over 15 years. This information is greatly needed to protect populations of wildebeest and their ranges. MaxEnt, a statistical model, was used to evaluate influential factors for wildebeest distribution and predict suitable habitats throughout the northern extent of the Serengeti National Park, the MMNR, and adjoining group ranches. There were thirty five abiotic and biotic variables used to create two distribution models in MaxEnt across the study area for two different time periods. Both models performed well with training AUCs >0.80. Precipitation seasonality, isothermality, and distances to lodges were the greatest contributing variables to wildebeest distribution in the November model. Kauth-Thomas wetness, annual temperature range, and distances to camps were significant factors for wildebeest distribution in the June model. Predictive maps from the June 2010 model revealed higher concentrations of predicted habitat suitability in areas historically impacted by the expansion of mechanized farming practices. It is recommended that the MMNR collaborate with local group ranch conservancies to secure seasonal dispersal sites for wildebeest and impose land use policies in unprotected areas. Results from MaxEnt also revealed that bioclimatic variables and soil and plant moisture are significant contributors to wildebeest distributions. The MMNR should evaluate the potential effects imposed by climate change to wildebeest distributions and populations. DETERMINING DRIVERS FOR WILDEBEEST (CONNOCHAETES TAURINUS) DISTRIBUTION IN THE MASAI MARA NATIONAL RESERVE AND SURROUNDING GROUP RANCHES
outputs Designing a mobile academic peer support system

Copyright and Moral Rights for the articles on this site are retained by the individual authors and/or other copyright owners. For more information on Open Research Online's data policy on reuse of materials please consult the policies page. In this paper, we discuss work in progress into the design of a mobile academic peer support system that enables 11-to-14 year old children to request and provide academic help to each other. Our proposed system was designed based on background research into the areas of peer learning, child development, help-seeking and academic motivation. Several methods, such as focus groups, interviews and Wizard of Oz, were used during the requirements gathering and initial testing stages. The proposed system is currently under development and will be tested in a study with school-pupils, over an extended period of time, in the next few months.
Convex Methods for Transduction

The 2-class transduction problem, as formulated by Vapnik [1], involves finding a separating hyperplane for a labelled data set that is also maximally distant from a given set of unlabelled test points. In this form, the problem has exponential computational complexity in the size of the working set. So far it has been attacked by means of integer programming techniques [2] that do not scale to reasonable problem sizes, or by local search procedures [3]. In this paper we present a relaxation of this task based on semi-definite programming (SDP), resulting in a convex optimization problem that has polynomial complexity in the size of the data set. The results are very encouraging for mid sized data sets, however the cost is still too high for large scale problems, due to the high dimensional search space. To this end, we restrict the feasible region by introducing an approximation based on solving an eigenproblem. With this approximation, the computational cost of the algorithm is such that problems with more than 1000 points can be treated.
Study of Routing Protocols for Wireless Sensor Networks

: Wireless sensor networks consist of plenty of nodes, which sense, compute and transmit certain physical quantities. These quantities are then transmitted to a recording station for obtaining inferences from the readings taken by those sensor nodes. For WSNs to work, connection & communication between nodes become important and thus, different routing techniques were proposed. The two main hurdles in designing a routing technique are - power management of the nodes and transmission speed of the nodes. Keeping in mind these two major problems, numerous routing protocols were given which depend upon the application and network topology. Out of the various routing protocols, LEACH (Low-Energy Adaptive Clustering Hierarchy) is one which belongs to hierarchal based routing techniques. Simulation of LEACH [1] protocol and its comparison with simple direct transmission method has been done on MATLAB-R2017a. From the results and the graphs obtained, it can be clearly understood that former is much better than the latter. In terms of network lifetime, first node death, transmission speed, data aggregation and on many other parameters, LEACH protocol, as in [1], outperforms basic direct routing protocol.
High Yield of RNA Sequencing for Targetable Kinase Fusions in Lung Adenocarcinomas with No Mitogenic Driver Alteration Detected by DNA Sequencing and Low Tumor Mutation Burden

Purpose: Targeted next-generation sequencing of DNA has become more widely used in the management of patients with lung adenocarcinoma; however, no clear mitogenic driver alteration is found in some cases. We evaluated the incremental benefit of targeted RNA sequencing (RNAseq) in the identification of gene fusions and MET exon 14 (METex14) alterations in DNA sequencing (DNAseq) driver–negative lung cancers. Experimental Design: Lung cancers driver negative by MSK-IMPACT underwent further analysis using a custom RNAseq panel (MSK-Fusion). Tumor mutation burden (TMB) was assessed as a potential prioritization criterion for targeted RNAseq. Results: As part of prospective clinical genomic testing, we profiled 2,522 lung adenocarcinomas using MSK-IMPACT, which identified 195 (7.7%) fusions and 119 (4.7%) METex14 alterations. Among 275 driver-negative cases with available tissue, 254 (92%) had sufficient material for RNAseq. A previously undetected alteration was identified in 14% (36/254) of cases, 33 of which were actionable (27 in-frame fusions, 6 METex14). Of these 33 patients, 10 then received matched targeted therapy, which achieved clinical benefit in 8 (80%). In the 32% (81/254) of DNAseq driver–negative cases with low TMB [0–5 mutations/Megabase (mut/Mb)], 25 (31%) were positive for previously undetected gene fusions on RNAseq, whereas, in 151 cases with TMB >5 mut/Mb, only 7% were positive for fusions (P < 0.0001). Conclusions: Targeted RNAseq assays should be used in all cases that appear driver negative by DNAseq assays to ensure comprehensive detection of actionable gene rearrangements. Furthermore, we observed a significant enrichment for fusions in DNAseq driver–negative samples with low TMB, supporting the prioritization of such cases for additional RNAseq. See related commentary by Davies and Aisner, p. 4586
Tracking of deformable contours by synthesis and match

This paper considers the problem of motion tracking of deformable contours based on synthesis and match. We propose framework which encodes specific information on shape, deformation and motion of the target object. Using this information, the trackers synthesize contours that are most likely to describe the object in the current frame, and perform localization operations to select the best match templates. We present three trackers: the first imposes affine motion smoothness constraints, the second employs principal component analysis to synthesize a codebook of contour templates, while the third combines these ideas to synthesize templates along several major modes of motion. The resulting trackers require only a few parameters to characterize the motion. They are thus suitable for very low bit rate visual communication tasks. Preliminary applications in model-based coding have been attempted.
Quantile based histogram equalization for noise robust large vocabulary speech recognition

The noise robustness of automatic speech recognition systems can be improved by reducing an eventual mismatch between the training and test data distributions during feature extraction. Based on the quantiles of these distributions the parameters of transformation functions can be reliably estimated with small amounts of data. This paper will give a detailed review of quantile equalization applied to the Mel scaled filter bank, including considerations about the application in online systems and improvements through a second transformation step that combines neighboring filter channels. The recognition tests have shown that previous experimental observations on small vocabulary recognition tasks can be confirmed on the larger vocabulary Aurora 4 noisy Wall Street Journal database. The word error rate could be reduced from 45.7% to 25.5% (clean training) and from 19.5% to 17.0% (multicondition training).
Probing the structural basis for differential KCNQ1 modulation by KCNE1 and KCNE2

KCNE1 associates with KCNQ1 to increase its current amplitude and slow the activation gating process, creating the slow delayed rectifier channel that functions as a “repolarization reserve” in human heart. The transmembrane domain (TMD) of KCNE1 plays a key role in modulating KCNQ1 pore conductance and gating kinetics, and the extracellular juxtamembrane (EJM) region plays a modulatory role by interacting with the extracellular surface of KCNQ1. KCNE2 is also expressed in human heart and can associate with KCNQ1 to suppress its current amplitude and slow the deactivation gating process. KCNE1 and KCNE2 share the transmembrane topology and a high degree of sequence homology in TMD and surrounding regions. The structural basis for their distinctly different effects on KCNQ1 is not clear. To address this question, we apply cysteine (Cys) scanning mutagenesis to TMDs and EJMs of KCNE1 and KCNE2. We analyze the patterns of functional perturbation to identify high impact positions, and probe disulfide formation between engineered Cys side chains on KCNE subunits and native Cys on KCNQ1. We also use methanethiosulfonate reagents to probe the relationship between EJMs of KCNE subunits and KCNQ1. Our data suggest that the TMDs of both KCNE subunits are at about the same location but interact differently with KCNQ1. In particular, the much closer contact of KCNE2 TMD with KCNQ1, relative to that of KCNE1, is expected to impact the allosteric modulation of KCNQ1 pore conductance and may explain their differential effects on the KCNQ1 current amplitude. KCNE1 and KCNE2 also differ in the relationship between their EJMs and KCNQ1. Although the EJM of KCNE1 makes intimate contacts with KCNQ1, there appears to be a crevice between KCNQ1 and KCNE2. This putative crevice may perturb the electrical field around the voltage-sensing domain of KCNQ1, contributing to the differential effects of KCNE2 versus KCNE1 on KCNQ1 gating kinetics.