Miracle-dz/UniFAR-FTUs huggingface dataset:
p21WAF1/CIP1 Upregulation through the Stress Granule-Associated Protein CUGBP1 Confers Resistance to Bortezomib-Mediated Apoptosis

Background p21WAF1/CIP1 is a well known cyclin-dependent kinase inhibitor induced by various stress stimuli. Depending on the stress applied, p21 upregulation can either promote apoptosis or prevent against apoptotic injury. The stress-mediated induction of p21 involves not only its transcriptional activation but also its posttranscriptional regulation, mainly through stabilization of p21 mRNA levels. We have previously reported that the proteasome inhibitor MG132 induces the stabilization of p21 mRNA, which correlates with the formation of cytoplasmic RNA stress granules. The mechanism underlying p21 mRNA stabilization, however, remains unknown. Methodology/Principal Findings We identified the stress granules component CUGBP1 as a factor required for p21 mRNA stabilization following treatment with bortezomib ( = PS-341/Velcade). This peptide boronate inhibitor of the 26S proteasome is very efficient for the treatment of myelomas and other hematological tumors. However, solid tumors are sometimes refractory to bortezomib treatment. We found that depleting CUGBP1 in cancer cells prevents bortezomib-mediated p21 upregulation. FISH experiments combined to mRNA stability assays show that this effect is largely due to a mistargeting of p21 mRNA in stress granules leading to its degradation. Altering the expression of p21 itself, either by depleting CUGBP1 or p21, promotes bortezomib-mediated apoptosis. Conclusions/Significance We propose that one key mechanism by which apoptosis is inhibited upon treatment with chemotherapeutic drugs might involve upregulation of the p21 protein through CUGBP1.
2-[3-(1H-Benzimidazol-2-yl)propyl]-1H-benzimidazol-3-ium 3,5-dicarboxybenzoate–benzene-1,3,5-tricarboxylic acid–water (1/1/1)

The title compound, C17H17N4 +·C9H5O6 −·C9H6O6·H2O, contains a protonated 2,2′-(1,3-propanediyl)bis(1H-benzimidazole) cation, a deprotonated benzene-1,3,5-tricarboxylic acid anion, a neutral benzene-1,3,5-tricarboxylic acid molecule and a water molecule, which are linked together through N—H⋯O, O—H⋯O and weak C—H⋯O hydrogen bonds into almost double sheets parallel to (4 ). These hydrogen-bonded sheets are packed in the crystal with the formation of centrosymmetric voids of 25.5 Å3, which are filled by the water molecules.
Identification of the ADP-L-glycero-D-manno-heptose-6-epimerase (rfaD) and heptosyltransferase II (rfaF) biosynthesis genes from nontypeable Haemophilus influenzae 2019

Haemophilus influenzae is an important human pathogen. The lipooligosaccharide (LOS) of H. influenzae has been implicated as a virulence determinant. To better understand the assembly of LOS in nontypeable H. influenzae (NtHi), we have cloned and characterized the rfaD and rfaF genes of NtHi 2019, which encode the ADP-L-glycero-D-manno-heptose-6-epimerase and heptosyltransferase II enzymes, respectively. This cloning was accomplished by the complementation of Salmonella typhimurium lipopolysaccharide (LPS) biosynthesis gene mutants. These deep rough mutants are novobiocin susceptible until complemented with the appropriate gene. In this manner, we are able to use novobiocin resistance to select for specific NtHi LOS inner core biosynthesis genes. Such a screening system yielded a plasmid with a 4.8-kb insert. This plasmid was able to complement both rfaD and rfaF mutants of S. typhimurium. The LPS of these complemented strains appeared identical to the wild-type Salmonella LPS. The genes encoding the rfaD and rfaF genes from NtHi 2019 were sequenced and found to be similar to the analogous genes from S. typhimurium and Escherichia coli. The rfaD gene encodes a polypeptide of 35 kDa and the rfaF encodes a protein of 39 kDa, as demonstrated by in vitro transcription-translation studies. Isogenic mutants which demonstrated truncated LOS consistent with inner core biosynthesis mutants were constructed in the NtHi strain 2019. Primer extension analysis demonstrated the presence of a strong promoter upstream of rfaD but suggested only a very weak promoter upstream of rfaF. Complementation studies, however, suggest that the rfaF gene does have an independent promoter. Mass spectrometric analysis shows that the LOS molecules expressed by H. influenzae rfaD and rfaF mutant strains have identical molecular masses. Additional studies verified that in the rfaD mutant strain, D-glycero-D-manno-heptose is added to the LOS molecule in place of the usual L-glycero-D-manno-heptose. Finally, the genetic organizations of the inner core biosynthesis genes of S. typhimurium, E. coli, and several strains of H. influenzae were examined, and substantial differences were uncovered.
A Probabilistic Model for Estimating Defect-Limited Yield of ASICs

This paper summarizes 15 statistical yield models for estimating the defect-limited yield of Application-Specific Integrated Circuits (ASICs). Probabilistic modelling approaches were used to adjust for process nodes (PAF) and design complexity (DAF). An Excel-based calculator with 15 models was developed. Yield was estimated per ASIC, also per 5 circuit types in an ASIC, which include IO, Logic, Memory, Pure Analog, and High-speed Digital. The output yield values were adjusted based on design complexity and process nodes. Design adjustment factor (DAF) and process adjustment factor (PAF) were estimated and used as multipliers to adjust yield values. Three Bayesian networks were developed to show yield dependencies on design influencing factors, while a $2\mathrm{D}$ geometry model was constructed to simulate the yield due to particle landing at different technology nodes. The estimated results were validated by manufacturing test data from sort and final tests of 4 different ASICs. Estimated results for each case matched the actual with reasonable percentage of difference.
When, What, and How Much to Reward in Reinforcement Learning-Based Models of Cognition

Reinforcement learning approaches to cognitive modeling represent task acquisition as learning to choose the sequence of steps that accomplishes the task while maximizing a reward. However, an apparently unrecognized problem for modelers is choosing when, what, and how much to reward; that is, when (the moment: end of trial, subtask, or some other interval of task performance), what (the objective function: e.g., performance time or performance accuracy), and how much (the magnitude: with binary, categorical, or continuous values). In this article, we explore the problem space of these three parameters in the context of a task whose completion entails some combination of 36 state-action pairs, where all intermediate states (i.e., after the initial state and prior to the end state) represent progressive but partial completion of the task. Different choices produce profoundly different learning paths and outcomes, with the strongest effect for moment. Unfortunately, there is little discussion in the literature of the effect of such choices. This absence is disappointing, as the choice of when, what, and how much needs to be made by a modeler for every learning model.
Semi‐Automated Video Morphing

We explore creating smooth transitions between videos of different scenes. As in traditional image morphing, good spatial correspondence is crucial to prevent ghosting, especially at silhouettes. Video morphing presents added challenges. Because motions are often unsynchronized, temporal alignment is also necessary. Applying morphing to individual frames leads to discontinuities, so temporal coherence must be considered. Our approach is to optimize a full spatiotemporal mapping between the two videos. We reduce tedious interactions by letting the optimization derive the fine‐scale map given only sparse user‐specified constraints. For robustness, the optimization objective examines structural similarity of the video content. We demonstrate the approach on a variety of videos, obtaining results using few explicit correspondences.
MEMS reflective type variable optical attenuator using off-axis misalignment

This paper proposes a reflective type microelectromechanical system variable optical attenuator (MEMS VOA) which uses 45 degree tilted vertical movable mirror fabricated by a deep reactive ion etching (DRIE). The optical attenuation is generated by an optical axis offset controlled by the vertical mirror. Fibers are aligned passively on the vertical grooves which are formed at the same plane with the control actuator.
A smooth hybrid symbolic control for the formation of UAVs over a partitioned space

This paper presents and implements a smooth hybrid supervisory control mechanism for the formation of unmanned helicopters. A polar partitioning scheme is utilized to bisimilarly abstract the motion space to find a finite state model for the motion dynamics of UAVs. To implement this algorithm, a hierarchical control structure is introduced which uses a discrete supervisor on the top layer that is connected to the regulation layer via an interface layer. The implantation issues of the proposed algorithm are investigated and a control mechanism is introduced to smoothly transit over the partitioned space without any jump on the control signals while preserving the bisimulation relation between the abstract model and the original continuous system. Actual flight test results are presented to verify the algorithm and the control structure performance.
Stereo matching with occlusion detection using cost relaxation

This paper presents a new stereo algorithm for computing dense disparity maps from stereo image pairs by a global cost relaxation, realized as an optimization problem, where the disparity map is the momentary state of a dynamic process. Following the natural role model of the human visual system, we assign a set of possible disparities to each image pixel described by cooperating probability variables. In the first step a correlation-based similarity measure is performed to initialize the relaxation process. The relaxation itself is formulated as an optimization of a global cost function taking into account both the stereoscopic continuity constraint and considerations of the pixel similarity. A special formulation guarantees the existence of a unique cost minimum which can be easily and rapidly found by standard numerical procedures. In a post-processing step, occluded areas are detected and a sub-pixel precise disparity map is computed.
The Importance of the Inelastic and Elastic Structures of the Crust in Constraining Glacial Density, Mass Change, and Isostatic Adjustment From Geodetic Observations in Southeast Alaska

Elastic deformation of the solid Earth in response to ice mass loss offers a promising constraint on the density of glacial material lost. Further, the elastic response to modern deglaciation is important to constrain for studies of glacial isostatic adjustment to determine the mantle's structure and rheology. Models of this elastic uplift are commonly based on the 1‐D, seismically derived global average Preliminary Reference Earth Model and typically neglect uncertainties that can arise from regional differences in elastic structure from that of the global average, lateral heterogeneities within the region, and inelastic behavior of the crust. We quantify these uncertainties using an ensemble of 1‐D local elastic structure models and empirical relations for the effects of inelasticity in the upper ∼10 km of the crust. In Southeast Alaska, modeling elastic uplift rates with local elastic structures results in up to a 20–40% difference from those modeled with the Preliminary Reference Earth Model. Although these differences are limited to regions near to ice‐covered areas, they are comparable to the differences in uplift rates expected from the loss of firn versus loss of ice. Far from ice‐covered areas, where most of the region's GPS observations were made, these differences become insignificant and do not affect previous glacial isostatic adjustment studies in the region. The methods presented here are based on the globally available LITHO1.0 seismic model and open source software, and the approach of using an ensemble of 1‐D elastic structures can be easily adapted to other regions around the world.
Aerobactin Synthesis Genes iucA and iucC Contribute to the Pathogenicity of Avian Pathogenic Escherichia coli O2 Strain E058

Aerobactin genes are known to be present in virulent strains and absent from avirulent strains, but contributions of iucC and iucA, which are involved in aerobactin synthesis, to the pathogenicity of avian pathogenic Escherichia coli (APEC) have not been clarified. In this study, effects of double mutants (iucA/iutA or iucC/iutA) compared to those of single mutants (iucA, iucC or iutA) of aerobactin genes on the virulence of APEC strain E058 were examined both in vitro (aerobactin production, ingestion into HD-11 cells, survival in chicken serum) and in vivo (competitive growth against parental strain, colonization and persistence). In competitive co-infection assays, compared to the E058 parental strain, the E058ΔiucA mutant was significantly reduced in the liver, kidney, spleen (all P<0.01), heart and lung (both P<0.001). The E058ΔiutA mutant also was significantly reduced in the liver, lung, kidney (all P<0.01), heart and spleen (both P<0.001). The E058ΔiucC mutant was significantly attenuated in the heart and kidney (both P<0.05) and showed a remarkable reduction in the liver, spleen and lung (P<0.01); meanwhile, both E058ΔiucAΔiutA and E058ΔiucCΔiutA double mutants were sharply reduced as well (P<0.001). In colonization and persistence assays, compared with E058, recovered colonies of E058ΔiucA were significantly reduced from the lung, liver, spleen and kidney (P<0.01) and significantly reduced in the heart (P<0.001). E058ΔiutA was significantly reduced from the heart, lung, liver, spleen and kidney (P<0.01). E058ΔiucC, E058ΔiucAΔiutA and E058ΔiucCΔiutA were significantly decreased in all organs tested (P<0.001). These results suggest that iutA, iucA and iucC play important roles in the pathogenicity of APEC E058.
A robust, two‐parameter method for the extraction of drainage networks from high‐resolution digital elevation models (DEMs): Evaluation using synthetic and real‐world DEMs

In this article, a method for drainage network extraction from high‐resolution digital elevation models (DEMs; e.g., those derived from airborne laser swath mapping) is presented, which requires just two user‐defined parameters and is capable of handling discontinuous valley networks. The accuracy and robustness of the method are illustrated using synthetic valley networks that mimic the complexities of real landscapes and for which the true drainage network is known exactly by construction. The method involves six principal steps: optimal Wiener filtering to remove microtopographic noise, mapping of the contour curvature, identification of valley heads using a user‐defined contour‐curvature threshold criterion, routing of a unit discharge of water from each valley head using a multiple‐flow‐direction routing algorithm, removal of discontinuous reaches from the drainage network using a user‐defined discharge‐per‐upstream‐valley‐head threshold criterion, and thinning of the valley network to a single pixel width. The method yields accurate results using the same user‐defined parameters for the two field sites considered in this study, suggesting that for DEMs with resolution of approximately 1 m, the method has the ability to produce accurate results for a variety of landscapes by using the same parameter values used in this study.
Polygonization of non-manifold implicit surfaces

A method is presented to broaden implicit surface modeling. The implicit surfaces usually employed in computer graphics are two dimensional manifolds because they are defined by real-valued functions that impose a binary regionalization of space (i.e., an inside and an outside). When tiled, these surfaces yield edges of degree two. The new method allows the definition of implicit surfaces with boundaries (i.e., edges of degree one) and intersections (i.e., edges of degree three or more). These non-manifold implicit surfaces are defined by a multiple regionalization of space. The definition includes a list of those pairs of regions whose separating surface is of interest. Also presented is an implementation that converts a nonmanifold implicit surface definition into a collection of polygons. Although following conventional implicit surface polygonization, there are significant differences that are described in detail. Several example surfaces are defined and polygonized. CR
MIDGUT VOLVULUS CAUSING FETAL DEMISE IN UTERO

Intestinal malrotation has an incidence of 1 per 6000 live births. The most serious consequence of malrotation is volvulus. Midgut volvulus is a rare condition in which the small bowel and proximal colon twist around the superior mesenteric artery, leading to a high-grade proximal bowel obstruction and vascular compromise of the intestine, thereby leading to infarction of the involved intestine. Midgut volvulus rarely occcurs antenatally and is usually not lethal in utero. There are only 7 cases of intrauterine fetal demise caused by midgut volvulus reported in the literature. We report a case of intrauterine fetal demise at 38 weeks of gestation, due to cardiovascular failure and shock from midgut volvulus. Non-specific abnormalities, including ascites and dilated bowel, had been seen on the antenatal ultrasound from the 15th week of gestation. In addition to the volvulus, the fetus had intestinal atresia and arthrogryphosis.
F-cell shift and protein loss strongly affect validity of PV reductions indicated by Hb/Hct and plasma proteins.

Numerous studies have focused on alterations in plasma volume (PV) on interventions like quiet standing, exercise, or heat stress. However, no method seems capable of truly estimating the PV alteration. Therefore, an attempt was made to validate commonly used indexes of PV changes. Quiet standing was used to cause graded PV reductions estimated from hemoglobin and hematocrit (Hb/Hct) and from serum concentrations of total protein, albumin, and "large proteins" (LP; total protein minus albumin). Results indicated the following. 1) Hb/Hct, with the merit that the marker (erythrocyte) stays within the circulation, reflect accurately a small-to-moderate PV loss (</=10% of control PV). At large PV decrease (>/=15-20% of control), however, F-cell shift can cause Hb/Hct to underestimate the response by up to 25-30%. 2) Albumin and total protein underrate PV loss due to protein escape (mainly albumin) from the circulation. 3) LP also underestimate the PV decline due to protein escape but can often predict large PV reductions clearly better than Hb/Hct. 4) Prolonged standing can lead to pronounced 25% PV decline.
A simulation method for streaming electrification by direct current field analysis

A simulation method for evaluating potential and electric field distribution in an oil-filled transformer was developed. Potential distribution around the entrance of the oil duct should be carefully considered in view of the risk of static discharge. A large potential may be built up by negative charge current through highly resistive insulators due to charge separation caused by streaming electrification at the pressboard (PB) surface. At steady state in terms of both fluid dynamics and electrical conduction, a flow of the negative charge can be regarded as a constant current source distributed over the PB surface that flow into grounded conductors through resistive materials such as the solid/liquid insulation of PB and oil. As will be presented in another paper in this conference by the authors, the local streaming current can be obtained from the local shearing stress calculated by a fluid dynamics simulator. Using the wall current distribution calculated from the shearing stress model as a distributed current source, the electric field and potential distribution were calculated by a direct current field simulator.
Sensor Fusion and Machine Learning for Seated Movement Detection With Trunk Orthosis

Advanced assistive devices developed for activities of daily living use machine learning (ML) for motion intention detection using wearable sensors. Trunk assistive devices provide safety, balance, and independence for wheelchair users individuals who spend prolonged hours in sitting positions. We used ML for trunk movement intention detection with a trunk orthosis. Sensor fusion technique with four electromyography (EMG) and one inertial measurement unit (IMU) sensor signals are used to develop a three-level classification system. Forty participants engaged in seated trunk movement trials wearing the orthosis. The trials comprised 30 movements involving trunk flexion/extension, lateral bending, and axial rotation. The wrapper method was used to reduce essential EMG features. Ensemble (ES), k-nearest neighbors (KNN), and support vector machine ML classifiers were used. Twenty-six features (five EMG for each of four muscles and six for IMU) were used to develop ten individual ML models, resulting in an average accuracy of 95.44%. Eight models achieved the highest accuracy with the ES and two with KNN. The models were then cascaded to form a trunk motion detection system that achieved a test accuracy of 87.0%. The promising result of this study can be implemented for trunk motion recognition with active trunk orthosis.
A Square Root Map on Sturmian Words

We introduce a square root map on Sturmian words and study its properties. Given a Sturmian word of slope $\alpha$, there exists exactly six minimal squares in its language (a minimal square does not have a square as a proper prefix). A Sturmian word $s$ of slope $\alpha$ can be written as a product of these six minimal squares: $s = X_1^2 X_2^2 X_3^2 \cdots$. The square root of $s$ is defined to be the word $\sqrt{s} = X_1 X_2 X_3 \cdots$. The main result of this paper is that that $\sqrt{s}$ is also a Sturmian word of slope $\alpha$. Further, we characterize the Sturmian fixed points of the square root map, and we describe how to find the intercept of $\sqrt{s}$ and an occurrence of any prefix of $\sqrt{s}$ in $s$. Related to the square root map, we characterize the solutions of the word equation $X_1^2 X_2^2 \cdots X_n^2 = (X_1 X_2 \cdots X_n)^2$ in the language of Sturmian words of slope $\alpha$ where the words $X_i^2$ are minimal squares of slope $\alpha$. We also study the square root map in a more general setting. We explicitly construct an infinite set of non-Sturmian fixed points of the square root map. We show that the subshifts $\Omega$ generated by these words have a curious property: for all $w \in \Omega$ either $\sqrt{w} \in \Omega$ or $\sqrt{w}$ is periodic. In particular, the square root map can map an aperiodic word to a periodic word.
Optimization proposal of a standard-based patient monitoring platform for ubiquitous environments

This article describes the optimization of a patient telemonitoring platform based on the ISO/IEEE11073 (X73) standard to enable medical device interoperability. In order to achieve this, principal advantages and remaining improvements are evaluated to include in further upgrades towards the new profile evolution, oriented to ubiquitous environments and wearable devices (Personal Health Devices, X73-PHD), and opened to additional plug-and-play features and remote management. After evaluating the possibilities, we describe the platform porting process, a required step to adapt it to the new functionalities and allowing the development of end-to-end standard based systems. The paper details the implementation of the agent-manager architecture, particularized on the X73-PHD communication protocol between a Medical Device (MD) and a central gateway (Compute Engine, CE). Lastly, the obtained results are evaluated, oriented to constitute an X73-PHD tester to prove the challenges currently under discussion in the European Standardization Committee (CEN).