Miracle-dz/UniFAR-FTUs huggingface dataset:
Epidemiology of Gallbladder Cancer: An Update

Background: Carcinoma of the gallbladder is relatively rare tumor. It is characterized by selective geographical distribution and female preponderance. The disease is often detected late and has poor prognosis. Methods: An extensive search of literature was carried out on Pubmed to identified epidemiological studies on gallbladder cancer. The studies were subdivided by various known factors or those who have been investigated. Results: A total of 338 articles were reviewed. The proposed and investigated factors identified are chronic cholecystitis and cholelithiasis, racial ethical and genetic factors, dietary and life style factor, menstrual factor, carcinogens, occupational exposure, obesity, body mass index and many others. Conclusion: The results of the present review show that there is no consensus on the cause of gallbladder cancer. Most of the studies lack sufficient power to decisively conclude any of the factors studied as the cause.
Normalization effect of levodopa on hierarchical brain function in Parkinson’s disease

Abstract Hierarchical brain organization, in which the rich club and diverse club situate in core position, is critical for global information integration in the human brain network. Parkinson’s disease (PD), a common movement disorder, has been conceptualized as a network disorder. Levodopa is an effective treatment for PD. Whether there is a functional divergence in the hierarchical brain system under PD pathology, and how this divergence is regulated by immediate levodopa therapy, remains unknown. We constructed a functional network in 61 PD patients and 89 normal controls and applied graph theoretical analyses to examine the neural mechanism of levodopa short response from the perspective of brain hierarchical configuration. The results revealed the following: (a) PD patients exhibited disrupted function within rich-club organization, while the diverse club preserved function, indicating a differentiated brain topological organization in PD. (b) Along the rich-club derivate hierarchical system, PD patients showed impaired network properties within rich-club and feeder subnetworks, and decreased nodal degree centrality in rich-club and feeder nodes, along with increased nodal degree in peripheral nodes, suggesting distinct functional patterns in different types of nodes. And (c) levodopa could normalize the abnormal network architecture of the rich-club system. This study provides evidence for levodopa effects on the hierarchical brain system with divergent functions.
A Study of the Relationships among Hotel Corporate Social Responsibility, Service Value, and Customer Satisfaction: Focused on the Five Star Hotel in Seoul

cys9408@hannamil.net Abstract. The number of hotel users keeps increasing, while the consumption market and the demand for tourism have increased. Thus, hotels play a role to represent related regions. Particularly among disadvantaged and poor groups, however, there is still a common idea that a hotel is not a facility that everyone can easily have access to because of its high charge. Combined with the in-creasing interest in the pursuit of a fair society, the values of coexistence and co-prosperity are spreading, and related efforts and practices are being carried out. The results revealed as follows. First, the factor of public or social dimen-sion and legal order has a significant influence on quality value, price value, and customer satisfaction. Second, quality value and price value have significant influences on customer
Testing the parametric form of the volatility in continuous time diffusion models - a stochastic process approach

We present new tests for the form of the volatility function which are based on stochastic processes of the integrated volatility. We prove weak convergence of these processes to centered processes whose conditional distributions are Gaussian. In the case of testing for a constant volatility the limiting process are standard Brownian bridges. As a consequence an asymptotic distribution free test and bootstrap tests (for testing of a general parametric form) can easily be implemented. It is demonstrated that the new tests are more than the currently available procedures. The new approach is also demonstrated by means of a simulation study.
Toward a 2D high-performance multi-channel system for time-correlated single-photon counting applications

Time-Correlated Single Photon Counting (TCSPC) is acknowledged as one of the most effective techniques for measuring weak and fast optical signals, since it provides very high temporal resolution and sensitivity. Nevertheless, the long acquisition time needed to perform a measurement it’s still the main drawback. To overcome this limitation, multidimensional TCSPC systems have been developed, but they still suffer for a strong trade-off between performance and number of channels: the higher the number of channels, the poorer the performance. In this work we present the design of a complete TCSPC acquisition system which is meant to overcome this trade-off. Since the best state-of-the-art detectors and sensing circuits developed so far are designed with different technologies, following the same approach those circuits will be designed onto different chips to achieve the best performance from both sides. Through Silicon Vias (TSVs) will be investigated as a possible solution for connecting a custom technology SPAD array to a CMOS pick-up circuit. Since a high number of detectors will cause the count rate to saturate due to the limited transfer rate of a PC, the target throughput has been set to 10 Gb/s, well beyond the state of the art. Consequently, the number of acquisition chains has been tailored on the affordable throughput, and a dynamic-routing logic connects the detectors to this lower number of acquisition channels. Five fast Time-to-Amplitude Converters (TACs), able to reach 80 Mconv/s, have been designed to get high temporal resolution along with low dead time.
Heterogeneous Integration of Microfluidics on Printed Circuit Boards for Lab-on-Chip Applications

Author(s): Babikian, Sarkis | Advisor(s): Li, Guann-Pyng | Abstract: Microfluidic technology has important applications in Point-of-Care (POC) diagnostics, and in high throughput screening and sequencing through the introduction of small, automated and portable microfluidic devices commonly known as Lab-on-Chip (LOC) devices, and Micro Total Analysis System (µTAS). These devices can perform biochemical and fluidic assays in automated fashion, using smaller amounts of samples and in faster periods of time when compared to traditional methods. However, LOC devices require the integration of active fluidic components as well as a wide array of sensors and actuators on the chip, which has presented a significant challenge in the traditional methods of fabricating microfluidics. In this dissertation, the use of the Printed Circuit Board (PCB) is proposed as a heterogeneous integration platform for microfluidic LOC devices. A novel heterogeneous integration architecture is demonstrated that enables the integration of microfluidics, electronics and optics on PCBs, and promotes standardized, scaled and cost effective fabrication of LOC devices. The fabrication and integration processes are described by demonstrating several microfluidic LOC devices built on PCBs, and integrated with key LOC functions on the chip, such as sample preparation, analyte extraction, and optical detection.
Conflict-Based Local Search for Minimum Partition into Plane Subgraphs (CG Challenge)

This paper examines the approach taken by team gitastrophe in the CG:SHOP 2022 challenge. The challenge was to partition the edges of a geometric graph, with vertices represented by points in the plane and edges as straight lines, into the minimum number of planar subgraphs. We used a simple variation of a conflict optimizer strategy used by team Shadoks in the previous year’s CG:SHOP to rank second in the challenge.
Shadoks Approach to Minimum Partition into Plane Subgraphs (CG Challenge)

We explain the heuristics used by the Shadoks team to win first place in the CG:SHOP 2022 challenge that considers the minimum partition into plane subgraphs. The goal is to partition a set of segments into as few subsets as possible such that segments in the same subset do not cross each other. The challenge has given 225 instances containing between 2500 and 75000 segments. For every instance, our solution was the best among all 32 participating teams
Orientation control strategies and adaptation to a visuomotor perturbation in rotational hand movements

Computational approaches to biological motor control are used to discover the building blocks of human motor behavior. Models explaining features of human hand movements have been studied thoroughly, yet only a few studies attempted to explain the control of the orientation of the hand; instead, they mainly focus on the control of hand translation, predominantly in a single plane. In this study, we aimed to establish a basic understanding of the way humans control the orientation of their hands. We developed a quaternion-based score that quantifies the geodicity of rotational hand movements and evaluated it experimentally. In the first experiment participants performed a simple orientation-matching task with a robotic manipulator. We found that rotations are generally performed by following a geodesic in the quaternion hypersphere, which suggests that, similarly to translation, the orientation of the hand is centrally controlled. We also established a baseline for the study of human response to perturbed visual feedback of the orientation of the hand. In the subsequent second experiment we studied the adaptation of participants to visuomotor rotation that is applied on the hand’s rotation, and the transfer of the adaptation to a different initial orientation. We observed partial adaptation to the perturbation. The patterns of the transfer of the adaptation to a different initial orientation were consistent with the representation of the orientation in extrinsic coordinates. The results of the two experiments raise questions regarding the nature of central control of hand orientation. Discussion and intuitions from these results can be of benefit for many applications that involve fine manipulation of rigid bodies, such as teleoperation and neurorehabilitation. Author summary Daily motor actions, as simple as pouring a glass of wine or as complicated as playing a violin, require coordinated activation of multiple muscles that synchronize to produce a precise motion of the hand. Controlled by sensorimotor areas in the central nervous system, our muscles can translate and rotate our hand from one posture to another. Our study focused on the very basis of the control of orientation: we attempted to reveal which variables are centrally controlled when we rotate our hand. The discovery that simple rotations are generally performed along a geometrically optimal path established a baseline for studying the response to rotation-based perturbations. By visually remapping the orientation of the hand, we found that humans perceive their hand’s orientation in visual, rather than joint-based coordinates. These findings have implications for the design of human-centered control systems for teleoperation, where visual distortions may occur, and for the design of rehabilitation devices for people with motor impairments.
Ischemic Stroke and Dietary Vitamin B12 Deficiency in Old-Aged Females: Impaired Motor Function, Increased Ischemic Damage Size, and Changed Metabolite Profiles in Brain and Cecum Tissue

The global population is aging and the prevalence of age-related diseases, such as stroke, is predicted to increase. A vitamin B12 deficiency (vit. B12 def.) is common in the elderly, because of changes in metabolism. Clinical studies have reported that a vit. B12 def results in worse outcome after stroke, the mechanisms through which a vit. B12 def. changes the brain requires further investigation. This study investigated the role of vit. B12 def. on stroke outcome and mechanisms using aged female mice. Eighteen month old females were put on a control or vit. B12 def. diet for four weeks, after which an ischemic stroke was induced in the sensorimotor cortex. After damage, motor function was measured and animals were euthanized and tissues were collected for analysis. Vit. B12 def. animals had increased levels of total homocysteine in plasma and liver, choline levels were also increased in the liver. Vit. B12 def. animals had larger damage volume in brain tissue and more apoptosis. In the cecum, changes in creatinine and methylmalonic acid were observed in vit. B12 def. animals, pathway analysis showed dysfunction in B12 transport. Analysis of mitochondrial metabolomics in brain tissue showed reduced levels of metabolites involved in the TCA cycle in vit. B12 def animals. Meanwhile, pathway analysis showed significant, widespread dysfunction in phenylalanine, tyrosine, and tryptophan biosynthesis. Motor function after stroke was impaired in vit. B12 def. animals. A dietary vitamin B12 deficiency impairs motor function through increased apoptosis and changes in mitochondrial metabolism in brain tissue.
Fine-scale diversity of microbial communities due to satellite niches in boom and bust environments

Recent observations have revealed that closely related strains of the same microbial species can stably coexist in natural and laboratory settings subject to boom-and-bust dynamics and serial dilutions, respectively. However, the possible mechanisms enabling the coexistence of only a handful of strains, but not more, have thus far remained unknown. Here, using a consumer-resource model of microbial ecosystems, we propose that by differentiating on Monod parameters characterizing microbial growth rates in high and low nutrient conditions, strains can coexist in patterns similar to those observed. In our model, boom-and-bust environments create satellite niches due to resource concentrations varying in time. These satellite niches can be occupied by closely related strains, thereby enabling their coexistence. We demonstrate that this result is valid even in complex environments consisting of multiple resources and species. In these complex communities, each species partitions resources differently and creates separate sets of satellite niches for their own strains. While there is no theoretical limit to the number of coexisting strains, in our simulations, we always find between 1 and 3 strains coexisting, consistent with experiments and observations. Author summary Recent genomic data has exposed to us the remarkable spectrum of microbial diversity in natural communities surrounding us, which harbor not only hundreds of species, but also a handful of closely related strains within each of those species (termed “oligo-colonization”). While the mechanisms behind species coexistence are much better studied, the mechanisms behind the coexistence of closely related strains have remained understudied. Here, using a simple consumer-resource model, we show that if strains differ on their Monod growth parameters, they can coexist even on a single limiting resource, provided that the environments vary with time in boom-and-bust cycles. The Monod growth parameters describe how a strain’s growth rate changes with resource concentration, namely the half-maximal concentration and maximal growth rate. Simulations of our model show that both in simple and complex environments, even though an arbitrary number of strains can coexist, typically it is between 1 and 3 strains of a species that coexist over several randomly assembled communities, consistent with some experimental observations. This is because the allowed parameter space for coexistence shrinks significantly with the number of strains that coexist.
An essential experimental control for functional connectivity mapping with optogenetics

To establish functional connectivity between two candidate neurons that might form a circuit element, a common approach is to activate an optogenetic tool such as Chrimson in the candidate pre-synaptic neuron and monitor fluorescence of the calcium-sensitive indicator GCaMP in a candidate post-synaptic neuron. While performing such experiments, we found that low levels of leaky Chrimson expression can lead to strong artifactual GCaMP signals in presumptive postsynaptic neurons even when Chrimson is not intentionally expressed in any particular neurons. Withholding all-trans retinal, the chromophore required as a co-factor for Chrimson response to light, eliminates GCaMP signal but does not provide an experimental control for leaky Chrimson expression. Leaky Chrimson expression appears to be an inherent feature of current Chrimson transgenes, since artifactual connectivity was detected with Chrimson transgenes integrated into three different genomic locations (two insertions tested in larvae; a third insertion tested in the adult fly). These false-positive signals may complicate the interpretation of functional connectivity experiments. We illustrate how a no-Gal4 negative control improves interpretability of functional connectivity assays. We also propose a simple but effective procedure to identify experimental conditions that minimize potentially incorrect interpretations caused by leaky Chrimson expression.
LOMAR: LOcalization Microscopy Analysis in R

In single molecule localization microscopy data (SMLM), individual instances of a macromolecular complex come in the form of point sets. Particle averaging, which combines localization data from a large number of instances, is often used to overcome experimental noise and obtain a refined view of the underlying structure. However, SMLM point sets are often heterogeneous due to biological variations in the structure they represent and must be partitioned into groups with similar structure before averaging which calls for being able to compute structurally-relevant similarity measures between sets of points. Here we introduce LOMAR (LOcalization Microscopy Analysis in R) a software package for the R programming language that enables comparison of point sets through implementation of several point sets registration methods and similarity measures derived from topological data analysis. We demonstrate use of the package on real and simulated SMLM data of nuclear pore complexes.
coiaf: Directly estimating complexity of infection with allele frequencies

In malaria, individuals are often infected with different parasite strains; the complexity of infection (COI) is defined as the number of genetically distinct parasite strains in an individual. Changes in the mean COI in a population have been shown to be informative of changes in transmission intensity with a number of probabilistic likelihood and Bayesian models now developed to estimate the COI. However, rapid, direct measures based on heterozygosity or FwS do not properly represent the COI. In this work, we present two new methods that use easily calculated measures to directly estimate the COI from allele frequency data. Using a simulation framework, we show that our methods are computationally efficient and comparably accurate to current methods in the literature. Through a sensitivity analysis, we characterize how the bias and accuracy of our two methods are impacted by the distribution of parasite densities and the assumed sequencing depth and number of sampled loci. We further estimate the COI globally from Plasmodium falciparum sequencing data using our developed methods and compare the results against the literature. We show significant differences in estimated COI globally between continents and a weak relationship between malaria prevalence and COI. Author summary Computational models, used in conjunction with rapidly advancing sequencing technologies, are increasingly being used to help inform surveillance efforts and understand the epidemiological dynamics of malaria. One such important metric, the complexity of infection (COI), indirectly quantifies the level of transmission. Existing “gold-standard” COI measures rely on complex probabilistic likelihood and Bayesian models. As an alternative, we have developed the statistics and software package coiaf, which features two rapid, direct measures to estimate of the number of genetically distinct parasite strains in an individual (the COI). Our methods were evaluated using simulated data and subsequently compared to current “state-of-the-art” methods, yielding comparable results. Lastly, we examined the distribution of the COI in several locations across the world, identifying significant differences in COI between continents. coiaf, therefore, provides a new, promising framework for rapidly characterizing polyclonal infections.
Surrounding Traffic Matters: Increases in Traffic Volume Are Related to Changes in EEG Rhythms in Urban Cyclists

In this study, we used an oddball EEG bicycle paradigm to study how changes in urban environments elicit changes in EEG markers. Participants completed an auditory oddball task while riding in three different cycling lane environments. A low traffic condition where participants rode in a fully separated bike lane alongside a quiet residential street, an intermediate traffic condition where participants rode alongside a busy residential street in a painted lane, and a heavy traffic condition where participants rode alongside fast/heavy traffic on a shared-use path. Relative to the low traffic, heavy traffic was associated with faster reaction time and a trend towards reduced accuracy, and increased N1 amplitude evoked by the standard tones. We attribute this difference in N1 amplitude to different attentional demands evoked by the different traffic conditions. In this fashion, heavy traffic requires greater auditory filtering. Furthermore, we found no differences in P3 amplitude associated with the traffic conditions. We discuss the implications of mobile paradigms to study attention in real-world settings.
The Arabidopsis ATP-Binding Cassette E protein ABCE2 is a conserved component of the translation machinery

ATP-Binding Cassette E (ABCE) proteins dissociate cytoplasmic ribosomes after translation terminates, and contribute to ribosome recycling, thus linking translation termination to initiation. This function has been demonstrated to be essential in animals, fungi, and archaea, but remains unexplored in plants. In most species, ABCE is encoded by a single-copy gene; by contrast, Arabidopsis thaliana has two ABCE paralogs, of which ABCE2 seems to conserve the ancestral function. We isolated apiculata7-1 (api7-1), a viable, hypomorphic allele of ABCE2,which has a pleiotropic morphological phenotype reminiscent of mutations affecting ribosome biogenesis factors and ribosomal proteins. We also studied api7-2, a null, recessive lethal allele of ABCE2. Co-immunoprecipitation experiments showed that ABCE2 physically interacts with components of the translation machinery. An RNA-seq study of the api7-1 mutant showed increased responses to iron and sulfur starvation. We also found increased transcript levels of genes related to auxin signaling and metabolism. Our results support a conserved role for ABCE proteins in ribosome recycling in plants, as previously shown for the animal, fungal, and archaeal lineages. In plants, the ABCE2 protein seems important for general growth and vascular development, likely due to an indirect effect through auxin metabolism.