Miracle-dz/UniFAR-FTUs huggingface dataset:
Helicobacter pylori Biofilm Formation and Its Potential Role in Pathogenesis

SUMMARY Despite decades of effort, Helicobacter pylori infections remain difficult to treat. Over half of the world's population is infected by H. pylori, which is a major cause of duodenal and gastric ulcers as well as gastric cancer. During chronic infection, H. pylori localizes within the gastric mucosal layer, including deep within invaginations called glands; thanks to its impressive ability to survive despite the harsh acidic environment, it can persist for the host's lifetime. This ability to survive and persist in the stomach is associated with urease production, chemotactic motility, and the ability to adapt to the fluctuating environment. Additionally, biofilm formation has recently been suggested to play a role in colonization. Biofilms are surface-associated communities of bacteria that are embedded in a hydrated matrix of extracellular polymeric substances. Biofilms pose a substantial health risk and are key contributors to many chronic and recurrent infections. This link between biofilm-associated bacteria and chronic infections likely results from an increased tolerance to conventional antibiotic treatments as well as immune system action. The role of this biofilm mode in antimicrobial treatment failure and H. pylori survival has yet to be determined. Furthermore, relatively little is known about the H. pylori biofilm structure or the genes associated with this mode of growth. In this review, therefore, we aim to highlight recent findings concerning H. pylori biofilms and the molecular mechanism of their formation. Additionally, we discuss the potential roles of biofilms in the failure of antibiotic treatment and in infection recurrence.
Superresolution method for data deconvolution by superposition of point sources

In this work we present a new algorithm for data deconvolution that allows the retrieval of the target function with super-resolution with a simple approach that after a precis e measurement of the instrument response function (IRF), the measured data are fit by a superposition of point sources (SUPPOSe) of equal intensity. In this manner only the positions of the sources need to be determined by an algorithm that minimizes the norm of the difference between the measured data and the convolution of the superposed point sources with the IRF. An upper bound for the uncertainty in the position of the sources was derived and two very different experimental situations were used for the test (an optical spectrum and fluorescent microscopy images) showing excellent reconstructions and agreement with the predicted uncertainties, achieving {\lambda}/10 resolution for the microscope and a fivefold improvement in the spectral resolution for the spectrometer. The method also provides a way to determine the optimum number of sources to be used for the fit.
Constructions in Ramsey theory

We provide several constructions for problems in Ramsey theory. First, we prove a superexponential lower bound for the classical 4‐uniform Ramsey number r4(5,n) , and the same for the iterated (k−4) ‐fold logarithm of the k ‐uniform version rk(k+1,n) . This is the first improvement of the original exponential lower bound for r4(5,n) implicit in work of Erdős and Hajnal from 1972 and also improves the current best known bounds for larger k due to the authors. Second, we prove an upper bound for the hypergraph Erdős–Rogers function fk+1,k+2k(N) that is an iterated (k−13) ‐fold logarithm in N . This improves the previous upper bounds that were only logarithmic and addresses a question of Dudek and the first author that was reiterated by Conlon, Fox and Sudakov. Third, we generalize the results of Erdős and Hajnal about the 3‐uniform Ramsey number of K4 minus an edge versus a clique to k ‐uniform hypergraphs.
Multi-pattern Embedded Phase Shifting Using a High-Speed Projector for Fast and Accurate Dynamic 3D Measurement

The goal of this study is to achieve high-speed and high-accuracy 3D measurement of a moving object using phase shifting. Phase shifting is a multi-shot method that uses structured light and enables high-accuracy and highresolution measurement with few projections. However, this method requires projecting a multi-tone pattern, which causes the projection speed of the projector to become a bottleneck. This in turn makes performing high-speed measurements difficult. Furthermore, because phase shifting is a multi-shot method, reduced measurement accuracy for moving objects becomes another concern. In this study, we overcome these problems by using a newly developed highspeed projector. First, this projector enables high-speed 3D measurement, as it can project 8-bit tone images at frame rates of 1000fps. Second, proposed method improves the measurement accuracy of moving objects by enabling phase unwrapping, while minimizing the number of projected patterns through pattern embedding. Through experiments, we demonstrate that, by embedding a Gray-code pattern within an interval of 100ìs, we can measure a object moving at a speed of approximately 30-50cm/s with a frame rate of 500fps and an average error of less than 1mm.
Benzene risk assessment: does new evidence on myelodysplastic syndrome justify a new approach?

Abstract Epidemiologic findings play an important role in benzene risk assessment, which is utilized to guide the selection of recommended benzene exposure levels to prevent adverse health effects. For decades, excess leukemia risk, especially that in the Pliofilm® cohort, has been the focus of benzene risk assessment. While more stringent benzene standards, often ≤1 ppm, have been promulgated to protect workers from developing leukemia, recent epidemiologic studies have reported elevated risk of myelodysplastic syndrome (MDS). This report aims to examine whether the use of new data on MDS is scientifically warranted in future benzene risk assessments. First, we reviewed current benzene guidelines, regulations, and underlying risk assessments in developed countries. Second, we examined current epidemiologic literature on benzene and MDS, which identified seven studies with simultaneous measures of MDS risk and benzene exposure and 17 studies on MDS in populations potentially exposed to benzene. Next, we examined the potential of the MDS data to serve as the basis of future benzene risk assessments, by comparing its quality and risk estimates with those used in current benzene standards. We conclude from the current literature that there is strong evidence that MDS can be caused by benzene, and the MDS data from the pooled petroleum study should be further examined in future benzene risk assessments. We recommend that future MDS-based benzene risk assessment use total MDS as the endpoint, take into consideration the full exposure period, and examine a range of benzene exposure metrics, including the role of peak, intermittent benzene exposures.
Using Simpson's Paradox to Discover Interesting Patterns in Behavioral Data

We describe a data-driven discovery method that leverages Simpson's paradox to uncover interesting patterns in behavioral data. Our method systematically disaggregates data to identify subgroups within a population whose behavior deviates significantly from the rest of the population. Given an outcome of interest and a set of covariates, the method follows three steps. First, it disaggregates data into subgroups, by conditioning on a particular covariate, so as minimize the variation of the outcome within the subgroups. Next, it models the outcome as a linear function of another covariate, both in the subgroups and in the aggregate data. Finally, it compares trendsto identify disaggregations that produce subgroups with different behaviors from the aggregate.We illustrate the method by applying it to three real-world behavioral datasets, including Q\&A site Stack Exchange and online learning platforms Khan Academy and Duolingo.
Attention-based Hierarchical Neural Query Suggestion

Query suggestions help users of a search engine to refine their queries. Previous work on query suggestion has mainly focused on incorporating directly observable features such as query co-occurrence and semantic similarity. The structure of such features is often set manually, as a result of which hidden dependencies between queries and users may be ignored. We propose an AHNQS model that combines a hierarchical structure with a session-level neural network and a user-level neural network to model the short- and long-term search history of a user. An attention mechanism is used to capture user preferences. We quantify the improvements of AHNQS over state-of-the-art RNN-based query suggestion baselines on the AOL query log dataset, with improvements of up to 21.86% and 22.99% in terms of MRR@10 and Recall@10, respectively, over the state-of-the-art; improvements are especially large for short sessions.
An Optimization Method for Quantitative Impedance Tomography

A near-field ultrasonic tomography method providing high resolution imaging for soft tissue in the reflection mode is reported. When the Born approximation is valid, the main limitation of this method is that it requires an incident pulse with infinite bandwidth, whereas the incident pulses used in practice have a limited bandwidth, which makes quantitative reconstruction impossible. The reconstructed image is qualitative in the sense that it is a band-pass filtered reconstruction of the impedance distribution. An optimization method based on the use of the geometrical information provided by the tomographic reconstruction is developed to obtain the quantitative information required. The object was approximated locally by an equivalent canonical body, on the basis of the previous global estimation. The inversion procedure is then carried out using the minimization of a cost function, which is the average over frequency of the difference between the measured field scattered by the object and the estimated field scattered by the equivalent canonical body. Assuming the object to be homogeneous by regions, the last step consists of assigning the estimated local impedance value to the region of interest. When the geometry of the real body is almost canonical, the optimization method yields accurate impedance assessments.
Mithramycin A Alleviates Osteoarthritic Cartilage Destruction by Inhibiting HIF-2α Expression

Osteoarthritis (OA) is the most common and increasing joint disease worldwide. Current treatment for OA is limited to control of symptoms. The purpose of this study was to determine the effect of specificity protein 1 (SP1) inhibitor Mithramycin A (MitA) on chondrocyte catabolism and OA pathogenesis and to explore the underlying molecular mechanisms involving SP1 and other key factors that are critical for OA. Here, we show that MitA markedly inhibited expressions of matrix-degrading enzymes induced by pro-inflammatory cytokine interleukin-1β (IL-1β) in mouse primary chondrocytes. Intra-articular injection of MitA into mouse knee joint alleviated OA cartilage destruction induced by surgical destabilization of the medial meniscus (DMM). However, modulation of SP1 level in chondrocyte and mouse cartilage did not alter catabolic gene expression or cartilage integrity, respectively. Instead, MitA significantly impaired the expression of HIF-2α known to be critical for OA pathogenesis. Such reduction in expression of HIF-2α by MitA was caused by inhibition of NF-κB activation, at least in part. These results suggest that MitA can alleviate OA pathogenesis by suppressing NF-κB-HIF-2α pathway, thus providing insight into therapeutic strategy for OA.
The “less-is-more” in therapeutic antibodies: Afucosylated anti-cancer antibodies with enhanced antibody-dependent cellular cytotoxicity

ABSTRACT Therapeutic monoclonal antibodies are the fastest growing class of biological therapeutics for the treatment of various cancers and inflammatory disorders. In cancer immunotherapy, some IgG1 antibodies rely on the Fc-mediated immune effector function, antibody-dependent cellular cytotoxicity (ADCC), as the major mode of action to deplete tumor cells. It is well-known that this effector function is modulated by the N-linked glycosylation in the Fc region of the antibody. In particular, absence of core fucose on the Fc N-glycan has been shown to increase IgG1 Fc binding affinity to the FcγRIIIa present on immune effector cells such as natural killer cells and lead to enhanced ADCC activity. As such, various strategies have focused on producing afucosylated antibodies to improve therapeutic efficacy. This review discusses the relevance of antibody core fucosylation to ADCC, different strategies to produce afucosylated antibodies, and an update of afucosylated antibody drugs currently undergoing clinical trials as well as those that have been approved.
Round-Hashing for Data Storage: Distributed Servers and External-Memory Tables

This paper proposes round-hashing, which is suitable for data storage on distributed servers and for implementing external-memory tables in which each lookup retrieves at most a single block of external memory, using a stash. For data storage, round-hashing is like consistent hashing as it avoids a full rehashing of the keys when new servers are added. Experiments show that the speed to serve requests is tenfold or more than the state of the art. In distributed data storage, this guarantees better throughput for serving requests and, moreover, greatly reduces decision times for which data should move to new servers as rescanning data is much faster.
Multicomponent Domino Synthesis, Anticancer Activity and Molecular Modeling Simulation of Complex Dispirooxindolopyrrolidines

A series of spirooxindolopyrrolidine fused N-styrylpiperidone heterocyclic hybrids has been synthesized in excellent yield via a domino multicomponent protocol that involves one-pot three component 1,3-dipolar cycloaddition and concomitant enamine reactions performed in an inexpensive ionic liquid, namely 1-butyl-3-methylimidazolium bromide ([bmim]Br). Compounds thus synthesized were evaluated for their cytotoxicity against U-937 tumor cells. Interestingly; compounds 5i and 5m exhibited a better cytotoxicity than the anticancer drug bleomycin. In addition; the effect of the synthesized compounds on the nuclear morphology of U937 FaDu cells revealed that treatment with compounds 5a–m led to their apoptotic cell death.
Quality assurance protocol for superficial and deep hyperthermia systems established by the Hellenic Association of Medical Physicists (HAMP) in cooperation with the Hellenic Society of Oncologic Hyperthemia (HSOH): A study based on European Society for Hyperthermic Oncology (ESHO) quality assurance

PURPOSE During the last years hyperthermia is a developing therapeutic modality in Greece. Quality assurance (QA) procedures are essential for ensuring the correct operation of the hyperthermia system and therefore the selective heating of the tumor with minimum toxicity to the surrounding healthy tissues. The European Society for Hyperthermic Oncology (ESHO) has proposed QA guidelines for superficial as well as deep hyperthermia systems. The purpose of this study was to describe the adapted QA protocol for superficial and deep hyperthermia systems established in Greece. METHODS A working group was created by the Hellenic Association of Medical Physicists (HAMP) for the proposal of QA guidelines for superficial and deep hyperthermia systems. A review of the protocol proposed by ESHO, together with the existing protocols in other European and International centers, as well as protocols suggested by European or International organizations, was performed. Then, a protocol was suggested, describing procedures for QA according to the current technology and the existing equipment used in Greece. RESULTS A protocol describing the procedures for QA of superficial and deep hyperthermia systems was proposed. These procedures aim to evaluate the correct operation of the device, the thermometric system, the generator, the incorporated power meter and the applicators. It will also ensure the electrical safety of the devices. CONCLUSIONS The proposed protocol, applied by medical physicists in Greece, will ensure an efficient treatment with safety and minimum adverse effects. This protocol has been approved by the Hellenic Society of Oncologic Hyperthermia and the Hellenic Association of Medical Physicists.
The relationship of physicality and its underlying mapping

We understand how physical things work from our experience interacting with them. The cause-effect mapping instills our knowledge of interaction. We extend our knowledge of physical interactions when interacting with computing devices, especially when we do not have prior experience with those devices. But, the mapping of interaction in the digital world is not as straightforward as in the physical world. It is unclear how far the rules of physicality hold in the computing realm when the level and kind of feedback is not necessarily the same with physical effort? How do we cope when the underlying mapping is incoherent in relation to the physical control? In this paper, we report a study on Cruel Design. Its objectives are: i) to investigate the role of physicality in the physical-logical interaction, and ii) to observe the behaviors of users as incoherent mappings occur. Four conditions to illustrate the different design of mappings were presented to users. From the findings, the physical condition plays a more dominant role than having to remember the correct mapping of the logical states, and, inverting an action on the same controller (regardless the type of mapping) is the natural reaction to overshoot.
Enhanced Local Skeletal Muscle Oxidative Capacity and Microvascular Blood Flow Following 7-Day Ischemic Preconditioning in Healthy Humans

Ischemic preconditioning (IPC), which involves intermittent periods of ischemia followed by reperfusion, is an effective clinical intervention that reduces the risk of myocardial injury and confers ischemic tolerance to skeletal muscle. Repeated bouts of IPC have been shown to stimulate long-term changes vascular function, however, it is unclear what metabolic adaptations may occur locally in the muscle. Therefore, we investigated 7 days of bilateral lower limb IPC (4 × 5 min) above limb occlusion pressure (220 mmHg; n = 10), or sham (20 mmHg; n = 10), on local muscle oxidative capacity and microvascular blood flow. Oxidative capacity was measured using near-infrared spectroscopy (NIRS) during repeated short duration arterial occlusions (300 mmHg). Microvascular blood flow was assessed during the recovery from submaximal isometric plantar flexion exercises at 40 and 60% of maximal voluntary contraction (MVC). Following the intervention period, beyond the late phase of protection (72 h), muscle oxidative recovery kinetics were speeded by 13% (rate constant pre 2.89 ± 0.47 min-1 vs. post 3.32 ± 0.69 min-1; P < 0.05) and resting muscle oxygen consumption (mO2) was reduced by 16.4% (pre 0.39 ± 0.16%.s-1 vs. post 0.33 ± 0.14%.s-1; P < 0.05). During exercise, changes in deoxygenated hemoglobin (HHb) from rest to steady state were reduced at 40 and 60% MVC (16 and 12%, respectively, P < 0.05) despite similar measures of total hemoglobin (tHb). At the cessation of exercise, the time constant for recovery in oxygenated hemoglobin (O2Hb) was accelerated at 40 and 60% MVC (by 33 and 43%, respectively) suggesting enhanced reoxygenation in the muscle. No changes were reported for systemic measures of resting heart rate or blood pressure. In conclusion, repeated bouts of IPC over 7 consecutive days increased skeletal muscle oxidative capacity and microvascular muscle blood flow. These findings are consistent with enhanced mitochondrial and vascular function following repeated IPC and may be of clinical or sporting interest to enhance or offset reductions in muscle oxidative capacity.
Signal Identification Track Info Signal Group Info Backbone Generation Synergistic Routing Candidate Generation Complete ? Streak Output Y Primal-Dual Solution Update

As VLSI technology scales to deep sub-micron, design for interconnections becomes increasingly challenging. The traditional bus routing follows a sequential bit-by-bit order, and few works explicitly target inter-bit regularity for signal groups via multi-layer topology selection. To overcome these limitations, we present Streak, an efficient framework that combines topology generation and wire synthesis with a global view of optimization and constrained metal layer track resource allocation. In the framework, an identification stage decomposes binding groups into a set of representative objects; with the generated backbones, equivalent topologies are accompanied by the bits in every object; then a formulation guides the routing considering wire congestion and design regularity. Furthermore, a bottom-up clustering methodology based on layer prediction targets to enhance the routability; a post-refinement stage is developed to match the source-to-sink distance deviation among bits in one group. Experimental results using industrial benchmarks demonstrate the effectiveness of the proposed technique.
A Sense of Obligation: Cultural Differences in the Experience of Obligation

In this investigation of cultural differences in the experience of obligation, we distinguish between Confucian Role Ethics versus Relative Autonomy lay theories of motivation and illustrate them with data showing relevant cultural differences in both social judgments and intrapersonal experience. First, when judging others, Western European heritage culture (WEHC) participants (relative to Confucian heritage culture [CHC] participants) judged obligation-motivated actors more negatively than those motivated by agency (Study 1, N = 529). Second, in daily diary and situation sampling studies, CHC participants (relative to WEHC participants) perceived more congruency between their own agentic and obligated motivations, and more positive emotional associations with obligated motivations (Study 2, N = 200 and Study 3, N = 244). Agentic motivation, however, was universally associated with positive emotions. More research on a Role Ethics rather than Relative Autonomy conception of agency may improve our understanding of human motivation, especially across cultures.
MicroRNA-548 q is a novel oncogene and potential prognostic biomarker in human gastric cancer

Increasing evidence reveals that microRNAs (miRNAs), a class of short noncoding RNAs, are aberrantly expressed in gastric cancer (GC). The purpose of the present study is to dig out potential dysregulated miRNAs that are highly involved in GC development. Firstly, we performed miRNA expression profiling in a large CRC cohort from Gene Expression Ominus (GEO), GSE78091 test series. We identified 43 miRNAs that were differentially expressed. The reliability of miRNA expression profiles was further verified in carcinoma tissues and paired adjacent normal tissues from 93 GC patients using qRT-PCR. We found that the expression of miR-548q, which has not been reported previously in GC, was significantly increased in GC tissues and cell lines. Increased miR-548q expression was closely associated with aggressive clinicopathological variables and poor prognosis of GC patients. Moreover, miR-548q silencing noticeably inhibited proliferation, colony formation, migration and invasion in GC cell lines. Down-regulation of miR-548q also markedly repressed epithelial-mesenchymal transition (EMT) process, which is the major mechanism of cancer metastasis. Accordingly, we herein have delineated the oncogenic role of miR-548q in GC. Our results might provide a miRNA-based target for GC treatment.