Miracle-dz/UniFAR-FTUs huggingface dataset:
Design methodology for sample preparation on digital microfluidic biochips

Recent advances in digital microfluidic biochips have led to a promising future for miniaturized laboratories, with the associated advantages of high sensitivity and reconfigurability. As one of the front-end operations on digital microfluidic biochips, sample preparation plays an important role in biochemical assays and applications. For fast and high-throughput biochemical applications, it is critical to develop an automated design methodology for sample preparation. Prior work in this area does not provide solutions to the problem of design automation for sample preparation. Moreover, it is critical to ensure the correctness of droplets and recover from errors efficiently during sample preparation. Published work on error recovery is inefficient and impractical for sample preparation. Therefore, in this paper, we present an automated design methodology for sample preparation, including architectural synthesis, layout synthesis, and dynamic error recovery. The proposed algorithm is evaluated on real-life biochemical applications to demonstrate its effectiveness and efficiency. Compared to prior work, the proposed algorithm can achieve up to 48.39% reduction in sample preparation time.
Epigenetic Attenuation of Mitochondrial Superoxide Dismutase 2 in Pulmonary Arterial Hypertension: A Basis for Excessive Cell Proliferation and a New Therapeutic Target

Background— Excessive proliferation and impaired apoptosis of pulmonary artery (PA) smooth muscle cells (PASMCs) contribute to vascular obstruction in patients and fawn-hooded rats (FHRs) with PA hypertension (PAH). Expression and activity of mitochondrial superoxide dismutase-2 (SOD2), the major generator of H2O2, is known to be reduced in PAH; however, the mechanism and therapeutic relevance of this are unknown. Methods and Results— SOD2 expression in PASMCs is decreased in PAH patients and FHRs with PAH. FHR PASMCs have higher proliferation and lower apoptosis rates than Sprague-Dawley rat PASMCs. Moreover, FHR PASMCs have hyperpolarized mitochondria, low H2O2 production, and reduced cytoplasmic and mitochondrial redox state. Administration of SOD2 small interfering RNA to normal PASMCs recapitulates the FHR PAH phenotype, hyperpolarizing mitochondria, decreasing H2O2, and inhibiting caspase activity. Conversely, SOD2 overexpression in FHR PASMCs or therapy with the SOD-mimetic metalloporphyrin Mn(III)tetrakis (4-benzoic acid) porphyrin (MnTBAP) reverses the hyperproliferative PAH phenotype. Importantly, SOD-mimetic therapy regresses PAH in vivo. Investigation of the SOD2 gene revealed no mutation, suggesting a possible epigenetic dysregulation. Genomic bisulfite sequencing demonstrates selective hypermethylation of a CpG island in an enhancer region of intron 2 and another in the promoter. Differential methylation occurs selectively in PAs versus aortic SMCs and is reversed by the DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine, restoring both SOD2 expression and the ratio of proliferation to apoptosis. Expression of the enzymes that mediate gene methylation, DNA methyltransferases 1 and 3B, is upregulated in FHR lungs. Conclusions— Tissue-specific, epigenetic SOD2 deficiency initiates and sustains a heritable form of PAH by impairing redox signaling and creating a proliferative, apoptosis-resistant PASMC. SOD augmentation regresses experimental PAH. The discovery of an epigenetic component to PAH may offer new therapeutic targets.
Analysis of the inhibitors of apoptosis identifies BIRC3 as a facilitator of malignant progression in glioma

Gliomas, the most common primary brain tumor in humans, include a spectrum of disease. High-grade gliomas (HGG), such as glioblastoma, may arise from low-grade gliomas (LGG) that have a more indolent course. The process of malignant transformation (MT) of LGG to HGG is poorly understood but likely involves the activation of signaling programs that suppress apoptosis. We previously showed that Survivin (BIRC5) plays a role in malignant progression of glioma. Here, we investigated the role of the remaining members of the Inhibitors of Apoptosis (IAP) family on promoting MT in glioma. Utilizing expression data from the cancer genome atlas (TCGA), we identified BIRC3 as a key facilitator of MT from LGG to HGG. TCGA HGGs with high expression of BIRC 3 demonstrated a survival disadvantage and expression levels of BIRC3 were also significantly higher in TCGA HGG compared to TCGA LGG cases. We validated our findings from TCGA by using matched human specimens to show that BIRC expression is increased in HGG compared to their precursor LGG lesions. Using a unique murine model of glioma, we show that overexpression of BIRC3 promotes higher grade glioma and significantly reduces tumor-free survival in mice.
Organizational Mechanisms for Enhancing User Innovation in Information Technology

Fostering information technology innovation has assumed primacy in discussions of information systems management. Changes in the nature of available information technologies and their potential applications underscore the importance of creating new knowledge for deploying a technology within an organization rather than transferring such knowledge from external sources. Technology users remain a largely untapped source for such knowledge creation. This paper argues that deliberate organizational design actions in the form of mechanisms can enhance technology users' propensity to innovate in information technology. Specifically, a taxonomy of organizational mechanisms is developed based on the ability of various mechanisms to facilitate knowledge acquisition and knowledge conversion. The conceptual taxonomy is populated with specific design actions described in the literature utilizing a Delphi study. The effects of various classes of mechanisms on three key antecedents of user propensity to innovate in IT: technology cognizance, ability to explore a technology, and intention to explore a technology, are tested using a field study. Results provide support for the conceptual taxonomy. Implications for theory and practice are offered.
Domestication Gene Mlx and Its Partner Mondo Are Involved in Controlling the Larval Body Size and Cocoon Shell Weight of Bombyx mori

Bombyx mori was domesticated from Bombyx mandarina. The long-term domestication of the silkworm has brought about many remarkable changes to its body size and cocoon shell weight. However, the molecular mechanism underlying the improvement in the economic characteristics of this species during domestication remains unclear. In this study, we found that a transposable element (TE)—Bm1—was present in the upstream regulatory region of the Mlx (Max-like protein X) gene in wild silkworms but not in all domesticated silkworms. The absence of Bm1 caused an increase in the promoter activity and mRNA content of Mlx. Mlx and its partner Mondo belong to the bHLHZ transcription factors family and regulate nutrient metabolism. RNAi of Mlx and Mondo decreased the expression and promoter activity of glucose metabolism-related genes (trehalose transport (Tret), phosphofructokinase (PFK), and pyruvate kinase (PK)), lipogenic genes (Acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS)), and glutamine synthesis gene (Glutamine synthase 2, (GS2)). Furthermore, the transgenic overexpression of Mlx and Mondo in the fat body of silkworms increased the larval body size, cocoon shell weight, and egg number, but the silencing of the two genes resulted in the opposite phenotypes. Our results reveal the molecular mechanism of Mlx selection during domestication and its successful use in the molecular breeding of Bombyx mori.
Situated Modeling of Epistemic Puzzles

Situation theory is a mathematical theory of meaning introduced by Jon Barwise and John Perry. It has evoked great theoretical interest and motivated the framework of a few `computational' systems. PROSIT is the pioneering work in this direction. Unfortunately, there is a lack of real-life applications on these systems and this study is a preliminary attempt to remedy this deficiency. Here, we solve a group of epistemic puzzles using the constructs provided by PROSIT.
BERT-Based Prediction Model of Management Sales Forecast Error Using Japanese Firms' Earnings Meeting Transcripts

Earnings meeting transcripts contain valuable information relevant to investment decision-making, and reflect firm's future performance such as sales revenue forecasts. In this paper, we proposed a BERT-based model to predict whether the actual sales beat the forecast using long-text Japanese EM transcripts. According to the experiment results, our proposed method outperforms the five conventional methods with an improvement ≥ 4% in accuracy.
Rapid modulation of N-formyl chemotactic peptide receptors on the surface of human granulocytes: formation of high-affinity ligand- receptor complexes in transient association with cytoskeleton

When human granulocytes were exposed to 50 nM N-formyl-Met-Leu-[3H]Phe at 37 degrees C they rapidly formed ligand-receptor complexes that dissociated 50-100 times more slowly than those on cells initially exposed to the peptide at 4 degrees C. These complexes of apparent higher affinity were stable after detergent solubilization of the cells with Triton X-100. The complexes co-isolated with the detergent insoluble cytoskeletal residues and were free of the cytosolic and Golgi markers, lactate dehydrogenase and galactosyl transferase, respectively. After 5 s of exposure to f-Met-Leu-Phe, 2,000-3,000 molecules of ligand per cell were trapped in such complexes. Continued exposure resulted in capture of a maximum of 14,000 molecules per cell by 5 min. Exposure at 15 degrees C, a temperature at which endocytosis of the receptor is prevented, resulted in complex formation at a linear rate for at least 20 min to levels twice those measured at 37 degrees C. At 4 degrees C, complex formation was approximately 10% of the maximum amount formed at 37 degrees C. Pulse-chase experiments revealed that the complex was in transient association with the cytoskeleton with a half life ranging between 30 s to 4 min depending on the length of the original incubation. Electron microscopic autoradiography indicated that after 1 min of incubation at 37 degrees C, the majority of the specific autoradiographic grains were localized to the outer circumference of the cellular cytoskeleton. After 4 min of incubation, the grains were less frequent at the cytoskeleton periphery but still threefold enriched over a random cellular distribution. We conclude that a metabolically controlled modulation of the state of the N-formyl chemotactic peptide receptor occurs in the plasma membrane which may be the result of transient association of ligand-receptor complex and the cell cytoskeleton.
Use of Bacterial Artificial Chromosomes in Generating Targeted Mutations in Human and Mouse Cytomegaloviruses

Cloning of cytomegalovirus (CMV) genomes as bacterial artificial chromosomes (BAC) in E. coli and their manipulation using the techniques of bacterial genetics has greatly facilitated the construction of CMV mutants. This unit describes easily applicable procedures that allow rapid introduction of any kind of targeted mutation into BAC‐cloned CMV genomes. Protocols for the reconstitution of virus from isolated BAC DNA, preparation of a virus stock, and isolation and characterization of viral DNA are also included. Special emphasis is laid on description of critical steps and thorough characterization of the altered BACs.
A Bayesian Methodology for Systemic Risk Assessment in Financial Networks

We develop a Bayesian methodology for systemic risk assessment in financial networks such as the interbank market. Nodes represent participants in the network and weighted directed edges represent liabilities. Often, for every participant, only the total liabilities and total assets within this network are observable. However, systemic risk assessment needs the individual liabilities. We propose a model for the individual liabilities, which, following a Bayesian approach, we then condition on the observed total liabilities and assets and, potentially, on certain observed individual liabilities. We construct a Gibbs sampler to generate samples from this conditional distribution. These samples can be used in stress testing, giving probabilities for the outcomes of interest. As one application we derive default probabilities of individual banks and discuss their sensitivity with respect to prior information included to model the network. An R-package implementing the methodology is provided.
NAP , WCCN , a New Linear Kernel , and Keyword Weighting for the HMM Supervector Speaker Recognition System

We demonstrate the application of Nuisance Attribute Proje ction (NAP), Within-Class Covariance Normalization (WCCN) , a new standard kernel, and keyword weighting for the keyword based HMM supervector speaker recognition system. On our development set (SRE04 8-side training), we achieve 22.6% a nd 16.2% EER improvements using NAP and WCCN respectively, a 19.5% EER improvement using NAP and WCCN jointly, and a 8.6% DCF improvement using keyword weighting. We also demonstrate the lack of effectiveness of gender separation in our NAP training, and counter-intuitive results using various modifications to the NAP technique. On our non-development set (SRE05 8-side training), we achieve a 5.3% EER and 18.6% DCF improvement using NAP and keyword-weighting, and a 13.7% EER and 12.3% DCF improvement using WCCN.
The antagonistic modulation of Arp2/3 activity by N-WASP, WAVE2 and PICK1 defines dynamic changes in astrocyte morphology

Summary Astrocytes exhibit a complex, branched morphology, allowing them to functionally interact with numerous blood vessels, neighboring glial processes and neuronal elements, including synapses. They also respond to central nervous system (CNS) injury by a process known as astrogliosis, which involves morphological changes, including cell body hypertrophy and thickening of major processes. Following severe injury, astrocytes exhibit drastically reduced morphological complexity and collectively form a glial scar. The mechanistic details behind these morphological changes are unknown. Here, we investigate the regulation of the actin-nucleating Arp2/3 complex in controlling dynamic changes in astrocyte morphology. In contrast to other cell types, Arp2/3 inhibition drives the rapid expansion of astrocyte cell bodies and major processes. This intervention results in a reduced morphological complexity of astrocytes in both dissociated culture and in brain slices. We show that this expansion requires functional myosin II downstream of ROCK and RhoA. Knockdown of the Arp2/3 subunit Arp3 or the Arp2/3 activator N-WASP by siRNA also results in cell body expansion and reduced morphological complexity, whereas depleting WAVE2 specifically reduces the branching complexity of astrocyte processes. By contrast, knockdown of the Arp2/3 inhibitor PICK1 increases astrocyte branching complexity. Furthermore, astrocyte expansion induced by ischemic conditions is delayed by PICK1 knockdown or N-WASP overexpression. Our findings identify a new morphological outcome for Arp2/3 activation in restricting rather than promoting outwards movement of the plasma membrane in astrocytes. The Arp2/3 regulators PICK1, and N-WASP and WAVE2 function antagonistically to control the complexity of astrocyte branched morphology, and this mechanism underlies the morphological changes seen in astrocytes during their response to pathological insult.
Laser and vision based map building techniques for mobile robot navigation

We presents some preliminary results of the ongoing research with the final goal of building an autonomous mobile robot. To achieve this scope the mapping problem is an ineluctable one. This paper presents a visual mapping system which detects the same Speeded Up Robust Features (SURF) on the stereo pair images in order to obtain three dimensional point clouds at every robot location. The algorithm tracks the displacement of the identical features viewed from different positions to get back the robots positions. The Iterative Closest Point (ICP) algorithm is used to register the obtained landmarks in the feature based map of the entire environment. Also a mapping algorithm based on the laser system is presented which can detect the dynamic objects that are present in the robots field. The results of an indoor office environment experiments are shown.
BioEve Search: A Novel Framework to Facilitate Interactive Literature Search

Background. Recent advances in computational and biological methods in last two decades have remarkably changed the scale of biomedical research and with it began the unprecedented growth in both the production of biomedical data and amount of published literature discussing it. An automated extraction system coupled with a cognitive search and navigation service over these document collections would not only save time and effort, but also pave the way to discover hitherto unknown information implicitly conveyed in the texts. Results. We developed a novel framework (named “BioEve”) that seamlessly integrates Faceted Search (Information Retrieval) with Information Extraction module to provide an interactive search experience for the researchers in life sciences. It enables guided step-by-step search query refinement, by suggesting concepts and entities (like genes, drugs, and diseases) to quickly filter and modify search direction, and thereby facilitating an enriched paradigm where user can discover related concepts and keywords to search while information seeking. Conclusions. The BioEve Search framework makes it easier to enable scalable interactive search over large collection of textual articles and to discover knowledge hidden in thousands of biomedical literature articles with ease.
Reactive Jamming of the Helium Network

In this paper, we investigate the feasibility of jamming the Helium network devices in the presence of multiple hotspots. We introduce the Wolfpack algorithm, which identifies the minimum number of jammers that are needed, and their appropriate locations relative to the devices to be jammed. Theoretical analysis and experimental results highlight the risks, the resilience of hotspot redundancy to jamming attacks, and the edge that jammers can have with more powerful hardware.
Responses of the Sino‐atrial Node to Change in Pressure in the Sinus Node Artery

The sino-atrial node area was perfused selectively through the right atrial artery in 76 dogs. The relationship between changes in the blood pressure in this artery and sinus node rhythmicity was studied in 56 hearts in which the major blood supply to the sinus node artery came from the right atrial artery. A reciprocal relation was observed between changes of blood pressure in the sinus node artery and the sinus rate. Some characteristics were: (1) The negative chronotropic effect induced by raising the blood pressure was linearly related to the Degrees of pressure change and more prominent than the positive chronotropic effect induced by reducing the pressure. (2) This relationship was most prominent in a limited range between 20 and 100 mm Hg. (3) Dichloroisoproterenol, atropine, hexamethonium, reserpine and vagotomy did not modify these responses. It is concluded that this localized mechanosensitivity of the sinus node to changes in arterial pressure may be responsible for the regulation of the heart rate in the lower range of blood pressure and that complete regulation of the heart rate is achieved physiologically in combination with the reflexes through the carotid and aortic nerves.
A Novel In-Fiber Helical Long Period Grating With Small Period Inscribed by Femtosecond Laser for Twist Sensing With Comprehensive Performance

We reported a highly sensitive twist sensor based on a novel helical long period grating (HLPG), which was written in the core region of a single-mode fiber (SMF) by a femtosecond (fs) laser. Due to the helical refractive index (RI) modulation with a small period ( $20~ \mu \text{m}$ ), the transmission spectrum exhibits multiple resonant dips, which are due to the resonant coupling between the fundamental core mode and multiple high-order cladding modes, respectively. When grating suffers from torsion, the polarization state of the incident light and the inherent structure of the HLPG will change, leading to variations in the intensity of the dips with the twist angle. Since the selected dips of the optimized sample have distinct intensity response to the twist, the grating can achieve enhanced twist sensitivities of 18.93 dB/rad in the clockwise (CW) direction from 0° to 48° and −20.54 dB/rad in the counterclockwise (CCW) direction from 0° to -48° by the differential intensity demodulation method. Furthermore, the machine learning method (MLM) has been exploited to analyze more resonant dips that have discrepant responses to the twist angle, enabling the enlargement of the sensing range and the discrimination of the twist direction. Featured with high torsion sensitivity, high resolution ( $\sim 0.028^{\circ }$ ), compact size, ease of fabrication, polarization-dependent twist response, and twist direction discrimination ability, the proposed structure has potentials from soft robotics to artificial textiles.
Gyroscopic Precession In Motion Modelling Of Ball-Shaped Robots

This study discusses kinematic and dynamic precession models for a rolling ball with a finite contact area and a point contact respectively. In literature, both conventions have been applied. In this paper, we discuss in detail the kinematic and dynamic models to describe the ball precession and the radius of a circular rolling path. The kinematic model can be used if the contact area and friction coefficient are sufficient to prevent slippage. The dynamic precession model has significance in multi-body simulation environments handling rolling balls with ideal point contacts. We have applied both the kinematic and dynamic precession model to evaluate the no-slip condition of the existing GimBall-robot. According to the result, the necessity of an external precession torque may cause slipping at lower velocities than expected if ignoring this torque.
Improved Silicon Cochlea using Compatible Lateral Bipolar Transistors

Analog electronic cochlear models need exponentially scaled filters. CMOS Compatible Lateral Bipolar Transistors (CLBTs) can create exponentially scaled currents when biased using a resistive line with a voltage difference between both ends of the line. Since these CLBTs are independent of the CMOS threshold voltage, current sources implemented with CLBTs are much better matched than current sources created with MOS transistors operated in weak inversion. Measurements from integrated test chips are shown to verify the improved matching.
TNF-Related Apoptosis-Inducing Ligand: Non-Apoptotic Signalling

TNF-related apoptosis-inducing ligand (TRAIL or Apo2 or TNFSF10) belongs to the TNF superfamily. When bound to its agonistic receptors, TRAIL can induce apoptosis in tumour cells, while sparing healthy cells. Over the last three decades, this tumour selectivity has prompted many studies aiming at evaluating the anti-tumoral potential of TRAIL or its derivatives. Although most of these attempts have failed, so far, novel formulations are still being evaluated. However, emerging evidence indicates that TRAIL can also trigger a non-canonical signal transduction pathway that is likely to be detrimental for its use in oncology. Likewise, an increasing number of studies suggest that in some circumstances TRAIL can induce, via Death receptor 5 (DR5), tumour cell motility, potentially leading to and contributing to tumour metastasis. While the pro-apoptotic signal transduction machinery of TRAIL is well known from a mechanistic point of view, that of the non-canonical pathway is less understood. In this study, we the current state of knowledge of TRAIL non-canonical signalling.