Miracle-dz/UniFAR-FTUs huggingface dataset:
aCGH Analysis of Predictive Biomarkers for Response to Bevacizumab plus Oxaliplatin- or Irinotecan-Based Chemotherapy in Patients with Metastatic Colorectal Cancer.

BACKGROUND The randomized phase III study (WJOG4407G) showed equivalent efficacy between FOLFOX and FOLFIRI in combination with bevacizumab as the first-line treatment for metastatic colorectal cancer (mCRC). We studied whole genome copy number profiles using array-based comparative genomic hybridization (aCGH) analysis of tumor tissue samples obtained in this study. The aim of this study was to identify gene copy number alterations that could aid in selecting either FOLFOX or FOLFIRI in combination with bevacizumab for patients with mCRC. MATERIALS AND METHODS DNA was purified from 154 pretreatment formalin-fixed paraffin-embedded tissue samples (75 from the FOLFOX arm and 79 from the FOLFIRI arm) of 395 patients enrolled in the WJOG4407G trial and analyzed by aCGH. Genomic regions greater than 1.2-fold were regarded as copy number gain (CNG). RESULTS Patient characteristics between the treatment arms were well balanced except for tumor laterality (left side; 64% in FOLFOX arm and 80% in FOLFIRI arm, p = .07). FOLFIRI showed a trend toward better response rate (RR), progression-free survival (PFS) and overall survival (OS) than FOLFOX in the patients with CNG of chromosome 8q24.1 (Fisher's exact test, p = .134 for RR; interaction test, p = .102 for PFS and p = .003 for OS) and 8q24.2 (Fisher's exact test, p = .179 for RR; interaction test, p = .144 for PFS and p = .002 for OS). CONCLUSION Chromosome 8q24.1-q24.2 may contain genes that could potentially serve as predictive markers for selecting either FOLFOX or FOLFIRI in combination with bevacizumab for treatment of patients with mCRC. IMPLICATIONS FOR PRACTICE Bevacizumab has been used as a standard first-line treatment for patients with metastatic colorectal cancer (mCRC) in combination with either oxaliplatin-based or irinotecan-based chemotherapy. Until now, there has been no predictive marker to choose between the two combination chemotherapies. This array-based comparative genomic hybridization analysis revealed that the difference in therapeutic effect between the two combination chemotherapies is prominent in patients with mCRC with gene copy number gain in chromosome 8p24.1-p24.2. Such patients showed more favorable response and survival when treated with irinotecan-based combination chemotherapy. Overlapping genes commonly found in this region may be predictive biomarkers of the efficacy of the combination chemotherapy with bevacizumab.
CD137 (4-1BB) Signalosome: Complexity Is a Matter of TRAFs

CD137 (4-1BB, Tnsfr9) is a member of the TNF-receptor (TNFR) superfamily without known intrinsic enzymatic activity in its cytoplasmic domain. Hence, akin to other members of the TNFR family, it relies on the TNFR-Associated-Factor (TRAF) family of adaptor proteins to build the CD137 signalosome for transducing signals into the cell. Thus, upon CD137 activation by binding of CD137L trimers or by crosslinking with agonist monoclonal antibodies, TRAF1, TRAF2, and TRAF3 are readily recruited to the cytoplasmic domain of CD137, likely as homo- and/or heterotrimers with different configurations, initiating the construction of the CD137 signalosome. The formation of TRAF2-RING dimers between TRAF2 molecules from contiguous trimers would help to establish a multimeric structure of TRAF-trimers that is probably essential for CD137 signaling. In addition, available studies have identified a large number of proteins that are recruited to CD137:TRAF complexes including ubiquitin ligases and proteases, kinases, and modulatory proteins. Working in a coordinated fashion, these CD137-signalosomes will ultimately promote CD137-mediated T cell proliferation and survival and will endow T cells with stronger effector functions. Current evidence allows to envision the molecular events that might take place in the early stages of CD137-signalosome formation, underscoring the key roles of TRAFs and of K63 and K48-ubiquitination of target proteins in the signaling process. Understanding the composition and fine regulation of CD137-signalosomes assembly and disassembly will be key to improve the therapeutic activities of chimeric antigen receptors (CARs) encompassing the CD137 cytoplasmic domain and a new generation of CD137 agonists for the treatment of cancer.
Simultaneous 18F-fluciclovine Positron Emission Tomography and Magnetic Resonance Spectroscopic Imaging of Prostate Cancer

Purpose: To investigate the associations of metabolite levels derived from magnetic resonance spectroscopic imaging (MRSI) and 18F-fluciclovine positron emission tomography (PET) with prostate tissue characteristics. Methods: In a cohort of 19 high-risk prostate cancer patients that underwent simultaneous PET/MRI, we evaluated the diagnostic performance of MRSI and PET for discrimination of aggressive cancer lesions from healthy tissue and benign lesions. Data analysis comprised calculations of correlations of mean standardized uptake values (SUVmean), maximum SUV (SUVmax), and the MRSI-derived ratio of (total choline + spermine + creatine) to citrate (CSC/C). Whole-mount histopathology was used as gold standard. Results: The results showed a moderate significant correlation between both SUVmean and SUVmax with CSC/C ratio. Conclusions: We demonstrated that the simultaneous acquisition of 18F-fluciclovine PET and MRSI with an integrated PET/MRI system is feasible and a combination of these imaging modalities has potential to improve the diagnostic sensitivity and specificity of prostate cancer lesions.
Toward Estimating Task Execution Confidence for Robotic Bin-Picking Applications

We present an approach geared toward estimating task execution conﬁdence for robotic bin-picking applications. This requires estimating execution conﬁdence for all constituent subtasks including part recognition and pose estimation, sin-gulation, transport, and ﬁne positioning. This paper is focussed on computing associated conﬁdence parameters for the part recognition and pose estimation subtask. In particular, our approach allows a robot to evaluate how good the part recognition and pose estimation is, based on a conﬁdence-measure, and thereby determine whether to proceed with the task execution (part singulation) or to request help from a human in order to resolve the associated failure. The value of a mean-square distance metric at a local minimum where the part matching solution is found is used as a surrogate for the conﬁdence parameter. Experiments with a Baxter robot are used illustrate our approach.
Helicobacter pylori Infection is Associated with Occurrence of Proteinuria in Type 2 Diabetes Patients: A Systemic Review and Meta-Analysis

Background: Type 2 diabetes (T2DM) patients are susceptible to Helicobacter pylori (HP), and it has been reported that the occurrence of proteinuria is associated with HP infection in T2DM patients; however, this view remains controversial. This meta-analysis aimed to explore the association between HP infection and the occurrence of proteinuria in T2DM patients. In addition, we hope to provide some recommendations to readers in clinical or related fields. Methods: Our meta-analysis was conducted with the methodology of the Cochrane Collaboration. Search strategies were formulated by relevant professionals. Case–control studies that compared the occurrence of proteinuria in T2DM patients with and without HP infection were involved in our meta-analysis. Relevant English or Chinese studies were searched on online databases before 2018, including PubMed, the Cochrane library, Medline, Google Scholar, the China National Infrastructure, and Wanfang database. The search strategies were “diabetic proteinuria, diabetic microalbuminuria, diabetic albuminuria, diabetic kidney disease, diabetic renal dysfunction, diabetic renal disease, diabetic nephropathy, diabetic complications, and diabetic mellitus, combined with HP. ” The quality of these involved articles was separately assessed by two investigators using the Newcastle–Ottawa Scale (NOS). Odds ratios (ORs) and associated 95% confidence intervals (CIs) were extracted and pooled using fixed-effects models. Results: Seven studies involving 1029 participants were included. The quality of these seven articles was all above five stars as assessed by NOS, and there was no significant publication bias in our meta-analysis. We found that T2DM patients with HP infection had a 2.00 times higher risk of the occurrence of proteinuria than patients without HP infection (OR: 2.00, 95% CI: 1.48–2.69). Conclusions: Our analysis showed that HP infection was associated with the occurrence of proteinuria in T2DM patients. HP radical surgery might be a therapeutic option for protecting kidney function in patients with T2DM.
Towards a Cognitively-Based Analytic Model of Human Control of Swarms

Robotic swarms are nonlinear dynamical systems that benefit from the presence of human operators in realistic missions with changing goals and constraints. There has been recent interest in safe operations of robotic swarms under human control. Verification and validation techniques for these human-machine systems could be deployed to provide formal guarantees of safe performance. A current limitation that hinders practical significant applications of verification to human-machine systems is the lack of analytic models of the human operator that include realistic cognitive constraints. Our research aims to develop high fidelity analytic human models via abstraction of cognitive models based on ACT-R. In this paper, we report on results from the first step in this process. We designed a 2-choice control task of a robotic swarm, obtained data from human operators and compared the fit of these data to two analytic models and an ACT-R based cognitive model. We present the experimental results and discuss our future plans on how the analytic model will be derived from the cognitive model so that the whole human-swarm system could be amenable to verification techniques.
Ten‐year change in neighborhood socioeconomic status and colorectal cancer

A growing body of research has demonstrated that individuals who live in neighborhoods with more severe socioeconomic deprivation may have higher risks for colorectal cancer (CRC). However, previous studies have examined neighborhood socioeconomic status (SES) at only 1 point in time, and it is unclear whether changes in neighborhood SES also can influence the risks of CRC.
CD8+-T Cells With Specificity for a Model Antigen in Cardiomyocytes Can Become Activated After Transverse Aortic Constriction but Do Not Accelerate Progression to Heart Failure

Heart failure due to pressure overload is frequently associated with inflammation. In addition to inflammatory responses of the innate immune system, autoimmune reactions of the adaptive immune system appear to be triggered in subgroups of patients with heart failure as demonstrated by the presence of autoantibodies against myocardial antigens. Moreover, T cell-deficient and T cell-depleted mice have been reported to be protected from heart failure induced by transverse aortic constriction (TAC) and we have shown recently that CD4+-helper T cells with specificity for an antigen in cardiomyocytes accelerate TAC-induced heart failure. In this study, we set out to investigate the potential contribution of CD8+-cytotoxic T cells with specificity to a model antigen (ovalbumin, OVA) in cardiomyocytes to pressure overload-induced heart failure. In 78% of cMy-mOVA mice with cardiomyocyte-specific OVA expression, a low-grade OVA-specific cellular cytotoxicity was detected after TAC. Adoptive transfer of OVA-specific CD8+-T cells from T cell receptor transgenic OT-I mice before TAC did not increase the risk of OVA-specific autoimmunity in cMy-mOVA mice. After TAC, again 78% of the mice displayed an OVA-specific cytotoxicity with on average only a three-fold higher killing of OVA-expressing target cells. More CD8+ cells were present after TAC in the myocardium of cMy-mOVA mice with OT-I T cells (on average 17.5/mm2) than in mice that did not receive OVA-specific CD8+-T cells (3.6/mm2). However, the extent of fibrosis was similar in both groups. Functionally, as determined by echocardiography, the adoptive transfer of OVA-specific CD8+-T cells did not significantly accelerate the progression from hypertrophy to heart failure in cMy-mOVA mice. These findings argue therefore against a major impact of cytotoxic T cells with specificity for autoantigens of cardiomyocytes in pressure overload-induced heart failure.
Replicating urban dynamics by generating human-like agents from smartphone GPS data

This paper is the first work to replicate and simulate urban dynamics by learning individuals' decision-making processes and creating human-like agents from GPS data. We develop a novel agent model by learning from historical data via reinforcement learning techniques. We test our methodology in different scenarios at the citywide level using real world smartphone GPS data. Simulation results show that our agents can successfully learn and generate human-like travel activities. Furthermore, the performance of synthetic urban dynamics significantly outperforms existing methods.
Na-assisted fast growth of large single-crystal MoS2 on sapphire

Monolayer molybdenum sulfide (MoS2), a typical semiconducting transition metal dichalcogenide, has emerged as a perfect platform for next-generation electronics and optoelectronics due to its sizeable band gap and strong light–matter interactions. Nevertheless, the controlled growth of a monolayer MoS2 single-crystal with a large-domain size and high crystal quality still faces great challenges. Herein, we demonstrate the fast growth of a large-domain monolayer MoS2 on the c-plane sapphire substrate with the assistance of sodium chloride (NaCl) crystals as the intermediate promoter. Particularly, the volatilization temperature of the NaCl crystal and the growth temperature of MoS2 are established to be the key parameters that influence the growth efficiency of MoS2 at an optimized growth condition. Monolayer triangular MoS2 domain with an edge length ∼300 μm is obtained within 1 min, featured with a growth rate ∼5 μm s–1. The Na element from the NaCl crystal is found to be able to facilitate the two dimensional growth of monolayer MoS2. This work thus offers novel insights into the high-efficiency production of large-domain monolayer MoS2 on insulating growth substrates.
Robust Dynamic CPU Resource Provisioning in Virtualized Servers

We present robust dynamic resource allocation mechanisms to allocate application resources meeting Service Level Objectives (SLOs) agreed between cloud providers and customers. In fact, two filter-based robust controllers, i.e., <inline-formula><tex-math notation="LaTeX">$\mathcal {H}_{\infty }$</tex-math><alternatives><mml:math><mml:msub><mml:mi mathvariant="script">H</mml:mi><mml:mi>∞</mml:mi></mml:msub></mml:math><inline-graphic xlink:href="makridis-ieq1-2966972.gif"/></alternatives></inline-formula> filter and Maximum Correntropy Criterion Kalman filter (MCC-KF), are proposed. The controllers are self-adaptive, with process noise variances and covariances calculated using previous measurements within a time window. In the allocation process, a bounded client mean response time (<inline-formula><tex-math notation="LaTeX">$\mathop {\mathrm{mRT}}$</tex-math><alternatives><mml:math><mml:mi> mRT </mml:mi></mml:math><inline-graphic xlink:href="makridis-ieq2-2966972.gif"/></alternatives></inline-formula>) is maintained. Both controllers are deployed and evaluated on an experimental testbed hosting the RUBiS (Rice University Bidding System) auction benchmark web site. The proposed controllers offer improved performance under abrupt workload changes, shown via rigorous comparison with current state-of-the-art. On our experimental setup, the Single-Input-Single-Output (SISO) controllers can operate on the same server where the resource allocation is performed; while Multi-Input-Multi-Output (MIMO) controllers are on a separate server where all the data are collected for decision making. SISO controllers take decisions not dependent to other system states (servers), albeit MIMO controllers are characterized by increased communication overhead and potential delays. While SISO controllers offer improved performance over MIMO ones, the latter enable a more informed decision making framework for resource allocation problem of multi-tier applications.
Virtual Torque Sensor for Low-Cost RC Servo Motors Based on Dynamic System Identification Utilizing Parametric Constraints

We propose a novel virtual torque sensor for commercial low-cost radio-controlled (RC) servo motors. The virtual torque sensor has played an important role for conventional robots. It has been used for torque-required control applications such as human–robot interaction and under-actuated robots. However, most virtual torque sensors are based on the inversion of actuators or robot dynamics with the assumption that entire dynamics are known. This is not applicable to the RC servo motors that have unknown control structures. As RC servo motors enable researchers and hobbyists to create lightweight but high performance robots in an easy and cost-effective manner, the development of a virtual torque sensor for these motors is necessary. In this study, we propose a design method of a virtual torque sensor for RC servo motors. First, the virtual sensor is derived mathematically based on internal dynamic models with parametric constraints and compared to the conventional model. Second, a dedicated system identification method is developed for the proposed virtual sensor to implement the sensor in actual experiments. Finally, we compare experimental results with the measurements obtained by an actual sensor.
A Novel Perfusion System for Damage Control of Hyperkalemia in Swine

Introduction: The standard of care for refractory hyperkalemia is renal replacement therapy (RRT). However, traditional RRT requires specialized equipment, trained personnel, and large amounts of dialysate. It is therefore poorly suited for austere environments. We hypothesized that a simplified hemoperfusion system could control serum potassium concentration in a swine model of acute hyperkalemia. Methods: Ten pigs were anesthetized and instrumented. A dialysis catheter was inserted. After bilateral nephrectomy, animals received intravenous potassium chloride and were randomized to the control or treatment group. In both groups, blood was pumped through an extracorporeal circuit (EC) with an in-line hemodialyzer. In the treatment arm, ultrafiltrate from the hemodialyzer was diverted through cartridges containing novel potassium binding beads and returned to the EC. Blood samples were obtained every 30 min for 6 h. Results: Serum potassium concentration was significantly lower in the treatment than in the control group over time (P = 0.02). There was no difference in serum total calcium concentration for group or time (P = 0.13 and 0.44, respectively) or platelet count between groups or over time (P = 0.28 and 1, respectively). No significant EC thrombosis occurred. Two of five animals in the control group and none in the treatment group developed arrhythmias. All animals survived until end of experiment. Conclusions: A simplified hemoperfusion system removed potassium in a porcine model. In austere settings, this system could be used to temporize patients with hyperkalemia until evacuation to a facility with traditional RRT.
SAmPLIng ELUSIVE SPECIES In KArST EnVIronmEnTS: dESIgn And dEmogrAPhIC modELIng ConSIdErATIonS

One of the primary difficulties associated with populations endemic to cave ecosystems is estimating basic biological parameters such as abundance, survival, and recruitment. As many karst systems can be perturbed, determining estimates of demographic variables are central to evaluating whether anthropogenic or environmental influences cause variation in population distribution and trajectories. Currently, sampling design and inference methods for demographic parameters are readily available and widely applied to a range of terrestrial fauna. Our objective is to provide an overview of potential sampling designs and demographic estimation methodologies which would be amenable for use on a variety of subterranean species. We will discuss concepts associated with spatial and temporal constraints contingent on the biology of the species under study, provide examples of potential sampling designs applicable to subterranean systems, and outline estimation techniques addressing issues associated with estimation of observability, presence/absence, abundance, survival and recruitment estimation, and transience associated with temporary and permanent emigration. While general and applicable, few sampling designs or modeling applications have been applied to karst species, likely due to perceived difficulties associated with low species abundance, limited spatial and temporal distribution, and unobservable states. However, we suggest that further investigation be directed towards design and application of common estimation approaches to further our understanding of the fauna existing in subterranean ecosystems.
Design of Mobile Application Control based on Hand Gesture

In recent years, we have seen dramatic progress in the field of Hand Gesture Recognition, yet these applications have some drawback. Keeping in view the trend of making application more interactive and simple, easy to use as well as cost efficient, a Hand Gesture Recognition based system is developed to allow interactive control of application using hand gesture. This paper presents a framework for hand gesture recognition based system which controls the mobile application. The working of this framework is based on the information fusion of 3 Axis Accelerometer (ACC) and Surface Electromyography (SEMG) sensors. A Gaussian Mixture Model (GMM) and Fast Dynamic Time Warping Algorithm (FDTW) are utilised to get the final result. In addition the system including a wearable hand gesture sensing device which is worn on the forearm and an algorithmic framework for the smart phone to recognise the hand gesture. The Armband which is worn on the forearm is able to manipulate 11 predefined gesture or even the personalised ones. The results suggest that the developed prototype responded to each gesture within 300 ms on the mobile phone, with average accuracy of 96%.
The role of individual choice in the evolution of social complexity

Constant re-evaluation of social affiliations and shifting social network structures can profoundly affect the adaptive fitness of individuals within a population, as well as yielding super-additive effects felt by the population as a whole. To evaluate the impact of different social affiliation choices, and the relative ability of individuals to correctly assess the success of other individuals, we have created a set of mathematical models based on network centrality measures. We choose the hypothetical measures of “popularity”, “closeness” and “betweenness” to examine the resulting self-organizations of social groups. Our findings suggest that some different types of social behav iors can lead to the same levels of stability and organizational success, suggesting the possibility that complex organizations could have evolved from simpler ones without any change in the selective pressures acting on the population.