Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-wide analysis of expression quantitative trait loci identified potential lung cancer susceptibility variants among Asian populations

Even though genome-wide association studies (GWASs) have identified dozens of single nucleotide polymorphisms (SNPs) affecting the susceptibility to lung cancer, only a tiny fraction of heritability can be explained. Regulating the expression of surrounding genes is one of the important mechanisms for SNPs to exert their effect. So it is necessary to systematically evaluate the associations between expression quantitative trait loci (eQTL) and lung cancer risk. In this study, a two-stage case-control design was used to evaluate the associations of eQTL SNPs (eSNPs) defined by GTEx in normal lung tissues with the risk of lung cancer based on two GWAS datasets, including 7127 cases and 6818 controls. Promising variants were replicated in an independent population with 1026 lung cancer cases and 1006 controls. Functional annotations of the identified eSNPs and related genes were performed based on multiple public databases. Finally, we identified two potential eSNPs associated with the risk of lung cancer in 3q28 [rs505974, OR = 0.90 (0.86 - 0.94), P = 6.51 × 10-6] and 21q22.3 [rs79589812, OR = 1.38 (1.21 - 1.58), P = 2.46 × 10-6]. Subgroup analysis showed rs505974 might interact with smoking behaviour. Gene-set enrichment and pathway analysis revealed that rs505974 may affect the susceptibility to lung cancer via regulating the expression of CLDN16, which may be involved in the chemical carcinogenesis pathway, whereas rs79589812 may regulate the expression of SPATC1L, which may be involved in the base excision repair pathway. These results provide an overview of the associations between eSNPs and lung cancer in Asian populations.
Mechanisms of Resistance to the Contact-Dependent Bacteriocin CdzC/D in Caulobacter crescentus

Bacteriocins are commonly used by bacteria to kill neighboring cells that compete for resources. Although most bacteriocins are secreted, the aquatic, oligotrophic bacterium Caulobacter crescentus produces a two-peptide bacteriocin, CdzC/D, that remains attached to the outer membranes of cells, enabling contact-dependent killing of cells lacking the immunity protein CdzI. The receptor for CdzC/D has not previously been reported. Here, we describe a genetic screen for mutations that confer resistance to CdzC/D. One locus identified, perA, encodes a pentapeptide repeat protein that resides in the outer membrane of target cells, where it may act as the direct receptor for CdzC/D. Collectively, our results provide new insight into bacteriocin function and diversity. ABSTRACT The Cdz bacteriocin system allows the aquatic oligotrophic bacterium Caulobacter crescentus to kill closely related species in a contact-dependent manner. The toxin, which aggregates on the surfaces of producer cells, is composed of two small hydrophobic proteins, CdzC and CdzD, each bearing an extended glycine-zipper motif, that together induce inner membrane depolarization and kill target cells. To further characterize the mechanism of Cdz delivery and toxicity, we screened for mutations that render a target strain resistant to Cdz-mediated killing. These mutations mapped to four loci, including a TonB-dependent receptor, a three-gene operon (named zerRAB for zipper envelope resistance), and perA (for pentapeptide envelope resistance). Mutations in the zerRAB locus led to its overproduction and to potential changes in cell envelope composition, which may diminish the susceptibility of cells to Cdz toxins. The perA gene is also required to maintain a normal cell envelope, but our screen identified mutations that confer resistance to Cdz toxins without substantially affecting the cell envelope functions of PerA. We demonstrate that PerA, which encodes a pentapeptide repeat protein predicted to form a quadrilateral β-helix, localizes primarily to the outer membrane of cells, where it may serve as a receptor for the Cdz toxins. Collectively, these results provide new insights into the function and mechanisms of an atypical, contact-dependent bacteriocin system. IMPORTANCE Bacteriocins are commonly used by bacteria to kill neighboring cells that compete for resources. Although most bacteriocins are secreted, the aquatic, oligotrophic bacterium Caulobacter crescentus produces a two-peptide bacteriocin, CdzC/D, that remains attached to the outer membranes of cells, enabling contact-dependent killing of cells lacking the immunity protein CdzI. The receptor for CdzC/D has not previously been reported. Here, we describe a genetic screen for mutations that confer resistance to CdzC/D. One locus identified, perA, encodes a pentapeptide repeat protein that resides in the outer membrane of target cells, where it may act as the direct receptor for CdzC/D. Collectively, our results provide new insight into bacteriocin function and diversity.
Abnormal TDP‐43 function impairs activity‐dependent BDNF secretion, synaptic plasticity, and cognitive behavior through altered Sortilin splicing

Aberrant function of the RNA‐binding protein TDP‐43 has been causally linked to multiple neurodegenerative diseases. Due to its large number of targets, the mechanisms through which TDP‐43 malfunction cause disease are unclear. Here, we report that knockdown, aggregation, or disease‐associated mutation of TDP‐43 all impair intracellular sorting and activity‐dependent secretion of the neurotrophin brain‐derived neurotrophic factor (BDNF) through altered splicing of the trafficking receptor Sortilin. Adult mice lacking TDP‐43 specifically in hippocampal CA1 show memory impairment and synaptic plasticity defects that can be rescued by restoring Sortilin splicing or extracellular BDNF. Human neurons derived from patient iPSCs carrying mutated TDP‐43 also show altered Sortilin splicing and reduced levels of activity‐dependent BDNF secretion, which can be restored by correcting the mutation. We propose that major disease phenotypes caused by aberrant TDP‐43 activity may be explained by the abnormal function of a handful of critical proteins, such as BDNF.
In vitro digestion of bread: How is it influenced by the bolus characteristics?

This study aimed to understand the impact of in vitro oral processing methods on bolus formation and the kinetics of starch hydrolysis of refined white bread during in vitro gastrointestinal digestion. Four in vitro oral processing methods (i.e., cut, cut-and-pestle, blend, and grind) were performed at two levels of disintegration (less and more intensive) and compared with human mastication. Boluses prepared using the in vitro methods had a larger particle size (20-69 mm2 vs. 14 mm2 ), a higher moisture content (64-68% vs. 47%), a softer texture (1.3-2.3 N vs. 6.3 N) and a less adhesive surface (0.3-1.0 vs. 1.6 N•s) as compared to the in vivo masticated ones. Moreover, in vitro prepared blouses were digested more rapidly than in vivo masticated ones during the stimulated intestinal digestion from 150 min onward, with a higher hydrolysis rate (0.011-0.012 mg/mL • min vs. 0.010 mg/mL • min) and a higher equilibrium concentration of reducing sugar (5.5-6.3 mg/mL vs. 4.9 mg/mL). Among all the in vitro methods, the blending and grinding methods produced boluses that most closely resemble the in vivo masticated ones in terms of their physical characteristics. The blending method also produced boluses having the highest amount of reducing sugar released (6.32 mg/mL). The amount of reducing sugar present in the PBS buffer outside the dialysis tube might be controlled by the diffusion efficiency at the beginning of the digestion (≤120 min) and then be largely influenced by the particle size of the bolus in the latter stage of the digestion. PRACTICAL APPLICATION: Studying the in vitro starch amyloysis is valuable for predicting the postprandial glycemic potential of starchy food. This work provides novel insights on the role of in vitro oral processing in the prediction of the glycemic potential of carbohydrate-rich staple food. Blending method is recommended because of its ability to produce boluses with similar physical characteristics as the in vivo masticated boluses. But the excessive structural breakdown occurred during blending also resulted in a higher enzymatic accessibility and a higher rate of starch digestion. Further study is needed to propose a new in vitro method that stimulates multiple actions occurred during mastication (cutting, grinding, and shearing), in order to match both physical properties and digestion profiles. Moreover, the amount of artificial saliva added should be adjusted according to the specific type of food.
Smart Gateway Based Multi-Tier Service-Oriented Fog Computing Architecture for Achieving Ultra-Low Latency

Services are part of our daily activities, such as the emergence of new solutions powered by cutting-edge technologies such as Fog Computing. Fog computing, new ideas for the cloud in the network, is considered the suitable platforms for the Internet of Things services and many applications. This fog - cloud computing integration is not directly moving forward. Some services required ultra-low latency like e-Health, public safety. Unnecessary communication loads not only the core network but also the data center that it finds. To do this, fog nodes can pre-process the data before sending it to the cloud. Smart Gateways are suitable candidates for service deployment. This paper presents a design of a service-oriented architecture using smart gateways as fog nodes which reduce service latency.
Environmental risk limits for chlorpropham in water

Het RIVM heeft in opdracht van het ministerie van Infrastructuur en Milieu (I&M), milieurisicogrenzen voor chloorprofam in water bepaald. Chloorprofam is een onkruidbestrijdingsmiddel en wordt ook gebruikt om te voorkomen dat aardappelen voortijdig kiemen. De stof is opgenomen in de Regeling Monitoring Kader Richtlijn Water, waarin staat aan welke eisen oppervlaktewater in Nederland moet voldoen. De huidige norm voor chloorprofam is niet afgeleid volgens de meest recente methodiek, daarom moeten nieuwe waterkwaliteitsnormen worden vastgesteld. De Stuurgroep Stoffen stelt deze nieuwe normen vast op basis van de wetenschappelijke advieswaarden in dit rapport. Het Maximaal Toelaatbaar Risiconiveau (MTR) is de concentratie in water waarbij geen schadelijke effecten te verwachten zijn, gebaseerd op jaargemiddelde concentraties. Hiervoor zijn drie routes onderzocht: directe effecten op waterorganismen, indirecte effecten op vogels en zoogdieren via het eten van prooidieren en indirecte effecten op mensen via het eten van voedsel. De eerste van deze drie levert de laagste waarde en bepaalt daarmee het MTRwater(4 microgram per liter). De Maximaal Aanvaardbare Concentratie (MACeco, water), die het ecosysteem beschermt tegen kortdurende concentratiepieken, is 43 microgram per liter. Op basis van meetgegevens over 2009 en 2010 is er geen aanwijzing dat deze concentraties worden overschreden.
E3 Ubiquitin Ligases RNF20 and RNF40 Are Required for Double-Stranded Break (DSB) Repair: Evidence for Monoubiquitination of Histone H2B Lysine 120 as a Novel Axis of DSB Signaling and Repair

Histone posttranslational modifications play fundamental roles in the regulation of double-stranded DNA break (DSB) repair. RNF20/RNF40-mediated monoubiquitination of histone H2B on lysine 120 (H2Bub) has been suggested as a potential mediator of DSB repair, although the nature and function of this posttranslational modification remain enigmatic. ABSTRACT Histone posttranslational modifications play fundamental roles in the regulation of double-stranded DNA break (DSB) repair. RNF20/RNF40-mediated monoubiquitination of histone H2B on lysine 120 (H2Bub) has been suggested as a potential mediator of DSB repair, although the nature and function of this posttranslational modification remain enigmatic. In this report, we demonstrate that RNF20 and RNF40 are required for DSB repair leading to homologous recombination (HR) and class switch recombination, a process driven by nonhomologous end joining (NHEJ), in mouse B cells. These findings suggest a role for RNF20 and RNF40 in DSB repair proximal to NHEJ/HR pathway choice and likely in the signaling of DSBs. We found that DSBs led to a global increase in H2Bub but not the transcription-associated posttranslational modifications H3K4me3 and H3K79me2. We also found that H2AX phosphorylation was dispensable for H2Bub and that ATM and ATR jointly regulate ionizing radiation (IR)-induced H2Bub. Together, our results suggest that RNF20, RNF40, and H2Bub may represent a novel pathway for DSB sensing and repair.
Optimizing Power-Based Indoor Tracking System for Wireless Sensor Networks using ZigBee

Evolution of wireless and digital communication gives birth to the smaller but powerful battery-equipped devices which are easy to maintain and perform the desired tasks. ZigBee is a Wireless Personal Area Network (WPAN) used for home or indoor automation, collecting data for medical research by using the low power digital radios to handle the low data rate. In ZigBee network, sensor nodes are heterogeneously deployed and continuously moving. To detect and tracking of those sensor nodes are challenging in terms of accuracy, calculation time and energy consumption. In this paper, proposed system uses the Received Signal Strength Indication (RSSI) protocol for localization, trilateration for fetching the exact coordinates of sensor nodes and these protocols helps to overcome the problem which eventually led to prolonged sensor network, accurate localization.
Scalable Triangle Discovery Algorithm for Large Scale-Free Network with Limited Internal Memory

In complex network, the links among the nodes fabricate thousands of polygons, where triangles are the most foundamental ones. As more links are added to the network, more polygons are split to be triangles. Discovering the triangles can help understand the current status of the network. Due to the limitations of internal memory, discovering all the triangles in a large-scale real-world network, e.g., online social network (OSN), is challenging and has intrigued researchers for years. Currently, parallel computation frameworks, e.g., MapReduce, have been employed to address this issue. The last reducer is required to load all the neighbors of each node into internal memory, which causes “the curse of the last reducer. ” The scale-free characteristic in real-world networks furthur exacerbate the applicability of the parallel triangle discovery algorithms. The current efforts on this issue mainly focus on dividing a large network into several small subnetworks and later employ internal memory algorithms. In this paper, we address this issue from a different perspective by employing the power-law degree distribution in scale-free networks. We theoretically and empirically prove that one node in scale-free network has a limited number of neighbors with a higher degree. Employing this finding, an novel parallel triangle discovery algorithm called degree partition (DePart) is designed. Since only the portion of neighbors with higher degrees are loaded into internal memory in the reducers, DePart solves “the curse of the last reducer” problem and works efficiently in clusters with limited internal memory. We develop DePart using MapReduce framework and examine the performance of DePart on five large real-world networks. The empirical testing results demonstrate that DePart has a favorable tradeoff between internal memory and total disk space and outperforms the current state-of-the-art MapReduce-based triangle discovery algorithms.
Analysis of interconnection between central nervous and cardiovascular systems

In the paper the aspects of collaboration and interconnection between central nervous and cardiovascular systems are described. Existing methods to estimate the connectivity between HRV and EEG signals and corresponding up-to-date studies are reviewed. It can be affirmed that there is an apparent interconnection between central nervous and cardiovascular systems on the basis of exam-ined papers. But the definite method of assessment of this interconnection capable to take into account the underlying manner of this connection is yet to be defined. It was determined that further research should be directed into examination of non-linear connectivity between HRV and EEG signals, methods for non-linear connectivity assessment and comparison of their performance. On this basis the new ways to improve the current approaches are expounded. Reference 29, figures 1.
A low noise global shutter CMOS image sensor with multiple sampling

In general, the CMOS image sensor is used as a rolling shutter , but in recent years the demand for a CMOS image sensor as a global shutter is increasing in various cases. Many methods have been proposed as noise reduction methods for a global shutter, but most of them are for fixed pattern noise and not for random noise. In this paper, we propose a method to reduce random noise by multiple sampling.
Latent lip prints: how far a link to the suspect? -

Recent years have witnessed the emerging reliability of lip prints in the criminal justice system worldwide [1-6]. Lip prints are to be found at different locations practically and logically on those surfaces that lips are likely to have been in touch, for example on the cups, glasses, cigarettes, windows, tissue paper, clothing, and even pen caps [7]. Accurate recording of these prints can, sometimes, be a major lead to the suspect at crime scenes. Though fingerprints are the conventional means of identification, the uniqueness of lip prints cannot be denied [8-12]. The problem lies in accurately recording these lip prints, especially the latent lip prints. DineshShankar et al. emphasized that a standard and uniform procedure is required for the collection, development, and recording of the lip prints [13]. Cosmetic industry claims to have discovered long-lasting lipsticks which do not leave any trace or visible mark on any of the used surfaces, e.g. cups, glasses, or tissue papers [14,15]. The real challenge lies in developing these invisible prints. Some investigators have tried successfully using the same technique as are used for fingerprints development [14,15]. A recent study demonstrated the usefulness of latent lip print in personal identification using black fingerprint powder on the glass slab surface [16]. Latent prints are impressions caused by the transfer of body perspirations or oils present on finger ridges to the surfaces of an object [17]. Similarly, the vermilion border of the lips has minor salivary glands with sweat glands in between and the commissures also have sebaceous glands which together with the moisturizing done by the tongue leads to the possibility of latent lip prints [8,9]. Therefore, the present study was planned to contemplate the possibility of the development of latent lip prints so as to justify its use in apprehending the suspect. Very few studies have analyzed the relevance and significance of latent lip prints at the crime scene.
Separating Musical Audio Signals

As consumers move increasingly to multichannel and surround-sound reproduction of sound, and also perhaps wish to remix their music to suit their own tastes, there will be an increasing need for high quality automatic source separation to recover sound sources from legacy mono or 2-channel stereo recordings. In this Contribution, we will give an overview of some for audio source separation, and some of the remaining research challenges in this area.
Ranking Function Detection via SVM: A More General Method

The existence of a ranking function implies the termination of a loop. Different methods are designed for detection of different classes of ranking functions. Moreover, for loops with polynomial guards and polynomial assignments, existing complete solutions for detecting their ranking functions are mostly with bad complexity. In this paper, we propose an approach to the synthesis of ranking functions for loops via support vector machine (SVM). We transform the ranking function detection problem into a binary classification problem. Once ranking function templates are given, the SVM is used to learn the coefficients of the templates. In this way, candidate ranking functions can be obtained. Finally, existing verification tools are employed to certify the candidates. With our approach, multiple forms of loops can be handled, and multiple classes of ranking functions can be detected. The effectiveness is presented with experimental evidence. We can detect ranking functions (e.g., polynomial ranking functions and non-polynomial ranking functions) for given loops, especially for loops with fractional or radical update that existing tools may not be able to handle as far as we know.
Robust motion controller design for servo system with 2 mass characteristics

In motion control, the major sources of uncertainties are friction, stiffness, inertia and disturbances. These uncertainties should be taken into account by any high performance robust motion controller. Position and speed controllers for two-mass systems with different performances, ranges of applicability and of different complexity need to be used. The objective of the paper is to propose a motion controller for a high performance XY positioning table. The simulated overall system consists of two parts-a motion controller and an observer. A disturbance observer is added to improve the robustness of the overall system in addition to motion controller. The disturbance observer is added to a Kalman filter in order that the algorithm may have robustness against the measurement and system errors. Simulation results show that the proposed motion controller has superior robustness to the parameters variations as well as to the disturbance.
Exploration of Methodological and Participant-Related Influences on the Number of Artifacts in ERP Data

Event-related potential (ERP) data has low signal-to-noise ratio, requiring the conduction of a large number of trials in order to collect sufficient amounts of data for subsequent analysis. Therefore, it would be highly beneficial if researchers could minimize the number of artifacts that occur in the data, minimizing the number of discarded trials and the total number of trials needed. This study thus examined connections between the number of trials that have to be eliminated due to artifacts and a set of methodological variables, physical considerations, and individual differences. In half of the electroencephalography (EEG) data collection blocks, naïve undergraduate participants were asked not to blink for the duration of the block (approximately 2.5 minutes), but in the other half, the stimulus set included blinking cues to give participants a chance to blink during blocks. The number of artifacts did not differ based on whether participants were cued to blink during blocks nor which type of block participants experienced first. However, the first block had significantly more artifacts than other blocks, and the third block had significantly fewer. Participants who had previously known one or both investigators had significantly fewer artifacts in their data than participants who had not, but no significant relationship was found between the number of artifacts and any other individual difference or physical consideration examined. These results imply that researchers could preemptively reduce the number of artifacts in their EEG data by including practice blocks and recruiting friends or acquaintances for studies if possible. Based on subjective, unsolicited participant feedback, the authors also recommend having blink cues in data collection blocks in order to make the task more comfortable for participants. Future studies with similar aims could use different equipment setups, e.g. electrode caps, and experimental manipulation of individual difference factors, e.g. motivation and comfort.