Miracle-dz/UniFAR-FTUs huggingface dataset:
Broad adsorption of sepsis-related PAMP and DAMP molecules, mycotoxins, and cytokines from whole blood using CytoSorb® sorbent porous polymer beads

Objective Sepsis is defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. In sepsis and septic shock, pathogen-associated molecular pattern molecules (PAMPS), such as bacterial exotoxins, cause direct cellular damage and/or trigger an immune response in the host often leading to excessive cytokine production, a maladaptive systemic inflammatory response syndrome response (SIRS), and tissue damage that releases DAMPs, such as activated complement and HMGB-1, into the bloodstream causing further organ injury. Cytokine reduction using extracorporeal blood filtration has been correlated with improvement in survival and clinical outcomes in experimental studies and clinical reports, but the ability of this technology to reduce a broader range of inflammatory mediators has not been well-described. This study quantifies the size-selective adsorption of a wide range of sepsis-related inflammatory bacterial and fungal PAMPs, DAMPs and cytokines, in a single compartment, in vitro whole blood recirculation system. Measurements and main results Purified proteins were added to whole blood at clinically relevant concentrations and recirculated through a device filled with CytoSorb® hemoadsorbent polymer beads (CytoSorbents Corporation, USA) or control (no bead) device in vitro. Except for the TNF-α trimer, hemoadsorption through porous polymer bead devices reduced the levels of a broad spectrum of cytokines, DAMPS, PAMPS and mycotoxins by more than 50 percent. Conclusions This study demonstrates that CytoSorb® hemoadsorbent polymer beads efficiently remove a broad spectrum of toxic PAMPS and DAMPS from blood providing an additional means of reducing the uncontrolled inflammatory cascade that contributes to a maladaptive SIRS response, organ dysfunction and death in patients with a broad range of life-threatening inflammatory conditions such as sepsis, toxic shock syndrome, necrotizing fasciitis, and other severe inflammatory conditions.
Complex Autoregressive Time-Frequency Analysis: Estimation of Time-Varying Periodic Signal Components

Time-frequency representations of nonstationary signals have a wide range of geophysical applications, including seismics, seismology, volcanology, and astrophysics. In this article, we estimate a complex autoregressive (AR) model from a short time window of the analytic signal. The local power spectrum is the inverse of the spectrum of this AR model. Since the coefficients are complex, the time window can be shorter than for the real AR model, which requires more coefficients. This results in higher time-frequency resolution, as seen in a synthetic data examples with different signal components. The new technique also gives good results when computing the instantaneous average frequency (IAF) of marine seismic data. Applied to digitized and downloaded data from the Laser Interferometer Gravitational-Wave Observatory (LIGO) in Hanford, Washington, the result clearly shows the linear chirp associated with the merger of two black holes.
A paralogous pair of mammalian host restriction factors form a critical host barrier against poxvirus infection

Host restriction factors constitute a formidable barrier for viral replication to which many viruses have evolved counter-measures. Human SAMD9, a tumor suppressor and a restriction factor for poxviruses in cell lines, is antagonized by two classes of poxvirus proteins, represented by vaccinia virus (VACV) K1 and C7. A paralog of SAMD9, SAMD9L, is also encoded by some mammals, while only one of two paralogs is retained by others. Here, we show that SAMD9L functions similarly to SAMD9 as a restriction factor and that the two paralogs form a critical host barrier that poxviruses must overcome to establish infection. In mice, which naturally lack SAMD9, overcoming SAMD9L restriction with viral inhibitors is essential for poxvirus replication and pathogenesis. While a VACV deleted of both K1 and C7 (vK1L-C7L-) was restricted by mouse cells and highly attenuated in mice, its replication and virulence were completely restored in SAMD9L-/- mice. In humans, both SAMD9 and SAMD9L are poxvirus restriction factors, although the latter requires interferon induction in many cell types. While knockout of SAMD9 with Crispr-Cas9 was sufficient for abolishing the restriction for vK1L-C7L- in many human cells, knockout of both paralogs was required for abolishing the restriction in interferon-treated cells. Both paralogs are antagonized by VACV K1, C7 and C7 homologs from diverse mammalian poxviruses, but mouse SAMD9L is resistant to the C7 homolog encoded by a group of poxviruses with a narrow host range in ruminants, indicating that host species-specific difference in SAMD9/SAMD9L genes serves as a barrier for cross-species poxvirus transmission.
Modeling and Predicting Seasonal Influenza Transmission in Warm Regions Using Climatological Parameters

Background Influenza transmission is often associated with climatic factors. As the epidemic pattern varies geographically, the roles of climatic factors may not be unique. Previous in vivo studies revealed the direct effect of winter-like humidity on air-borne influenza transmission that dominates in regions with temperate climate, while influenza in the tropics is more effectively transmitted through direct contact. Methodology/Principal Findings Using time series model, we analyzed the role of climatic factors on the epidemiology of influenza transmission in two regions characterized by warm climate: Hong Kong (China) and Maricopa County (Arizona, USA). These two regions have comparable temperature but distinctly different rainfall. Specifically we employed Autoregressive Integrated Moving Average (ARIMA) model along with climatic parameters as measured from ground stations and NASA satellites. Our studies showed that including the climatic variables as input series result in models with better performance than the univariate model where the influenza cases depend only on its past values and error signal. The best model for Hong Kong influenza was obtained when Land Surface Temperature (LST), rainfall and relative humidity were included as input series. Meanwhile for Maricopa County we found that including either maximum atmospheric pressure or mean air temperature gave the most improvement in the model performances. Conclusions/Significance Our results showed that including the environmental variables generally increases the prediction capability. Therefore, for countries without advanced influenza surveillance systems, environmental variables can be used for estimating influenza transmission at present and in the near future.
Analysis of the interaction between the retinal ON and OFF channels using CNN‐UM models

Quantitative retinal modeling is an important tool for analyzing the circuitry underlying the functional organization of the retina, and developing neuromorphic signal processing for retinal prostheses. The Cellular Neural Network (CNN) is a suitable tool for both purposes due to its structure. Using multilayer CNN models we analyzed two phenomena: First the signal distortion caused by nonlinear synapses and secondly the use of inhibitory interaction between ON and OFF channels. Our simulations show that the ON–OFF interaction can reduce the signal distortion caused by nonlinear synapses. Copyright © 2008 John Wiley & Sons, Ltd.
Joint Clusters and Iterative Graph Cuts for ALS Point Cloud Filtering

A novel method that combines joint clusters and iterative graph cuts for ALS point cloud filtering is proposed in this paper. The method first extracts clusters of points from the raw point cloud, and then classifies ground points at the cluster level. There are four main steps, i.e., two-step point cloud clustering, critical point extraction, initial terrain determination, and terrain densification based on iterative graph cuts. Smooth clusters, rough clusters, and scattered points are extracted by the two-step clustering to depict the raw point cloud, which reduces the complexity of raw data and the judgment difficulty in the subsequent procedures. Critical points of each cluster are extracted, and the initial terrain is determined among the smooth clusters. Using the initial terrain and critical points, iterative graph cuts is performed to segment ground and nonground points at the cluster level. Experiments on ISPRS dataset with a low point density and Utah dataset with a moderate point density show that our approach provides a satisfactory trade off between Type I and Type II errors. Moreover, our method significantly outperforms progressive TIN densification based filters, and successfully controls Type II errors.
Polymorphism rs2682818 in miR‐618 is associated with colorectal cancer susceptibility in a Han Chinese population

MicroRNAs (miRNAs), endogenous small noncoding RNAs (ncRNAs), play crucial roles in cancer development. Many studies have demonstrated that miRNAs can serve as diagnostic and therapeutic biomarkers for malignancies. Additionally, single nucleotide polymorphisms (SNPs) located in miRNA functional regions have been reported to be involved in cancer susceptibility. In this study, we investigated the associations between SNPs located in miRNA functional regions and colorectal cancer (CRC) susceptibility. We systematically screened all candidate miRNAs and their SNPs and then evaluated the relationships between the SNPs and CRC susceptibility in a Han Chinese population including 878 patients with CRC and 884 controls. Genotyping was performed by TaqMan assay. After comprehensively screening the miRNAs and SNPs, we elected to evaluate the association between SNP rs2682818 in miR‐618 and CRC susceptibility. We found that the AA and AC/AA genotypes of rs2682818 were associated with a decreased risk of CRC compared with the CC genotype (odds ratio (OR) = 0.54, 95% confidence interval (CI) = 0.37–0.79 for AA vs. CC in codominant model; OR = 0.82, 95% CI = 0.68–0.99 for AC/AA vs. CC in dominant model). However, we obtained no statically significant results in our subgroup analyses. SNP rs2682818 in miR‐618 has potential as a biomarker for individuals with high CRC susceptibility. Our findings need to be verified in studies including larger samples. Moreover, molecular functional studies of miR‐681 must be performed to confirm its relationship with CRC.
Regulation of MiR-146a and TRAF6 in the Diagnose of Lupus Nephritis

Background Lupus nephritis (LN) is a major complication of systemic lupus erythematosus (SLE). This study tested miR-146a and its target gene TRAF6 expression in LN patients and discussed their relationship with LN. Material/Methods One hundred twenty-eight LN patients and 30 healthy controls were enrolled in this study. MiR-146a and TRAF6 expression in peripheral blood mononuclear cells (PBMCs) were detected. Serum cytokines content was determined by ELISA. The diagnostic role of miR-146a and TRAF6 in LN activity was evaluated by ROC curve. The impact of miR-146a and TRAF6 on end-stage renal disease (ESRD) was compared by survival curve. The effect of miR-146a and TRAF6 on LN recurrence was analyzed. Results Compared with healthy controls, miR-146a expression was significantly reduced and TRAF6 was upregulated in LN patients. The expression was related to LN activity. MiR-146a expression was negatively correlated, whereas TRAF6 was positively correlated with serum IL-1β, IL-6, IL-8, and TNF-α activity. The area under the ROC curve (AUC) of miR-146a and TRAF6 on the diagnosis of LN was 0.821 and 0.897, respectively. The AUC of miR-146a and TRAF6 on LN activity differentiation was 0.921 and 0.872, respectively. Downregulation of miR-146a and upregulation of TRAF6 increased the incidence of ESRD progression. Downregulation of miR-146a and upregulation of TRAF6 elevated the possibility of recurrence within one year. Conclusions MiR-146a declined, while TRAF6 increased in LN patients compared with healthy controls. Their expression can be used to effectively differentiate LN and evaluate activity. MiR-146a reduction and TRAF6 upregulation increased the possibility of ESRD progress and recurrence within one year.
Correlation between the Severity of Obstructive Sleep Apnea and Heart Rate Variability Indices

The risk of cardiovascular disease is known to be increased in obstructive sleep apnea syndrome (OSAS). Its mechanism can be explained by the observation that the sympathetic tone increases due to repetitive apneas accompanied by hypoxias and arousals during sleep. Heart rate variability (HRV) representing cardiac autonomic function is mediated by respiratory sinus arrhythmia, baroreflex-related fluctuation, and thermoregulation-related fluctuation. We evaluated the heart rate variability of OSAS patients during night to assess their relationship with the severity of the symptoms. We studied overnight polysomnographies of 59 male untreated OSAS patients with moderate to severe symptoms (mean age 45.4± 11.7 yr, apnea-hypopnea index [AHI]=43.2±23.4 events per hour, and AHI >15). Moderate (mean age 47.1±9.4 yr, AHI=15-30, n=22) and severe (mean age 44.5±12.9 yr, AHI >30, n=37) OSAS patients were compared for the indices derived from time and frequency domain analysis of HRV, AHI, oxygen desaturation event index (ODI), arousal index (ArI), and sleep parameters. As a result, the severe OSAS group showed higher mean powers of total frequency (TF) (p=0.012), very low frequency (VLF) (p= 0.038), and low frequency (LF) (p=0.002) than the moderate OSAS group. The LF/HF ratio (p=0.005) was higher in the severe group compared to that of the moderate group. On the time domain analysis, the HRV triangular index (p=0.026) of severe OSAS group was significantly higher. AHI was correlated best with the LF/HF ratio (rp=0.610, p<0.001) of all the HRV indices. According to the results, the frequency domain indices tended to reveal the difference between the groups better than time domain indices. Especially the LF/HF ratio was thought to be the most useful parameter to estimate the degree of AHI in OSAS patients.
The Adomian decomposition method for solving delay differential equation

A numerical method based on the Adomian decomposition method which has been developed by Adomian [Adomian, G. (1994). Solving Frontier Problems of Physics: The Decomposition Method. Kluwer Academic Publishers, Boston, MA] is introduced in this paper for the approximate solution of delay differential equations. The algorithm is illustrated by studying an initial value problem. The results obtained are presented and show that only a few terms are required to obtain an approximate solution which is found to be accurate and efficient.
Optimal line of hepatotomy for left lateral living donor liver transplantation according to the anatomical variations of left hepatic duct system

Multiple duct anastomoses during LLS transplantation increase the incidence of biliary complications. The optimal plane of hepatotomy that results in the least number of bile ducts at the surface was investigated according to LHD variations. Ducts of 30 human livers were injected with resin and LHD branching on 3D‐CT reconstructions were analyzed. Ducts on the virtual hepatotomy surface were estimated in three splitting lines. Variations with subtypes were described. Ia (66.7%): ducts from segments (S.) II–III form a common trunk and S.IV duct joins it. Ib (10%): common trunk formed by ducts from S.II–S.III while S.IV duct joins the common hepatic duct. IIa (16.67%): S.IV duct drains into S.III duct. IIc (3.33%): S.IV duct drains into both S.II and S.III ducts. III (3.33%): trifurcation of S.II, S.III and S.IV ducts. When the virtual hepatotomy line was on the FL, there was a single duct for the anastomosis in 30% of cases but two, three, or four ducts in 53.3%, 10%, and 3.3%, respectively. Division 1 cm to the right of the FL resulted in one duct (70%), but S.IV duct injury may occur. LLS hepatotomy should not necessarily be performed along the FL. Variations must be taken into consideration to minimize the number of biliary anastomoses during liver implantation.
A Potential Role of the 5-HTTLPR Polymorphism in Self-Reported Executive Functioning

Abstract Intense effort is directed toward searching for associations between genes and neuropsychological measures of executive functions. In contrast, the impact of genetic polymorphisms on self-rating of everyday executive functioning has not been investigated so far. This study was designed to test associations of self-reported executive functioning, measured with the Behavior Rating Inventory of Executive Function (BRIEF-A), with dopaminergic and serotoninergic genes in non-clinical population and to assess impact of neuropsychological and personality characteristics on these associations. One hundred healthy adults completed the BRIEF-A, personality inventories SPQ-74, STAI, MMPI, and neuropsychological tests for executive functions. Polymorphisms in the DRD4, COMT, DRD2, HTR2A, and SLC6A4 genes were genotyped. We revealed a significant main effect of the SLC6A4’s 5-HTTLPR polymorphism on BRIEF-A scores (F = 2.21, P = .018, η2 = .24). Among the BRIEF-A measures, the genotype effect was significant for the Plan/Organize (F = 7.34, P = .008, η2 = .07) and Task Monitor scales (F = 4.33, P = .04, η2 = .04), and the Metacognition index (F = 4.21, P = .043, η2 = .04). Carriers of the short allele reported fewer problems than homozygotes for the long allele. Correlations of the BRIEF-A measures with neuropsychological variables were weak, while those with personality characteristics were strong, with trait anxiety being the most powerful predictor of the BRIEF-A scores. However, the relationship between the 5-HTTLPR and BRIEF-A scores remained significant when trait anxiety was controlled for. The results suggest a potential role of the 5-HTTLPR in self-reported everyday task planning and monitoring.
MglC, a Paralog of Myxococcus xanthus GTPase-Activating Protein MglB, Plays a Divergent Role in Motility Regulation

ABSTRACT In order to optimize interactions with their environment and one another, bacteria regulate their motility. In the case of the rod-shaped cells of Myxococcus xanthus, regulated motility is essential for social behaviors. M. xanthus moves over surfaces using type IV pilus-dependent motility and gliding motility. These two motility systems are coordinated by a protein module that controls cell polarity and consists of three polarly localized proteins, the small G protein MglA, the cognate MglA GTPase-activating protein MglB, and the response regulator RomR. Cellular reversals are induced by the Frz chemosensory system, and the output response regulator of this system, FrzZ, interfaces with the MglA/MglB/RomR module to invert cell polarity. Using a computational approach, we identify a paralog of MglB, MXAN_5770 (MglC). Genetic epistasis experiments demonstrate that MglC functions in the same pathway as MglA, MglB, RomR, and FrzZ and is important for regulating cellular reversals. Like MglB, MglC localizes to the cell poles asymmetrically and with a large cluster at the lagging pole. Correct polar localization of MglC depends on RomR and MglB. Consistently, MglC interacts directly with MglB and the C-terminal output domain of RomR, and we identified a surface of MglC that is necessary for the interaction with MglB and for MglC function. Together, our findings identify an additional member of the M. xanthus polarity module involved in regulating motility and demonstrate how gene duplication followed by functional divergence can add a layer of control to the complex cellular processes of motility and motility regulation. IMPORTANCE Gene duplication and the subsequent divergence of the duplicated genes are important evolutionary mechanisms for increasing both biological complexity and regulation of biological processes. The bacterium Myxococcus xanthus is a soil bacterium with an unusually large genome that carries out several social processes, including predation of other bacterial species and formation of multicellular, spore-filled fruiting bodies. One feature of the large M. xanthus genome is that it contains many gene duplications. Here, we compare the products of one example of gene duplication and divergence, in which a paralog of the cognate MglA GTPase-activating protein MglB has acquired a different and opposing role in the regulation of cellular polarity and motility, processes critical to the bacterium's social behaviors.
Improving lazy abstraction for SCR specifications through constraint relaxation

Formal requirements specifications, eg, software cost reduction (SCR) specifications, are challenging to analyse using automated techniques such as model checking. Since such specifications are meant to capture requirements, they tend to refer to real‐world magnitudes often characterized through variables over large domains. At the same time, they feature a high degree of nondeterminism, as opposed to other analysis contexts such as (sequential) program verification. This makes model checking of SCR specifications difficult even for symbolic approaches. Moreover, automated abstraction refinement techniques such as counterexample guided abstraction refinement fail in many cases in this context, since the concrete state space is typically large, and reaching specific states of interest may require complex executions involving many different states, causing these approaches to perform many abstraction refinements, and making them ineffective in practice. In this paper, an approach to tackle the above situation, through a 2‐stage abstraction, is presented. The specification is first relaxed, by disregarding the constraints imposed in the specification by physical laws or by the environment, before being fed to a counterexample guided abstraction refinement procedure, tailored to SCR. By relaxing the original specification, shorter spurious counterexamples are produced, favouring the abstraction refinement through the introduction of fewer abstraction predicates. Then, when a counterexample is concretizable with respect to the relaxed (concrete) specification but it is spurious with respect to the original specification, an efficient though incomplete refinement step is applied to the constraints, to cause the removal of the spurious case. This approach is experimentally assessed, comparing it with related techniques in the verification of properties and in automated test case generation, using various SCR specifications drawn from the literature as case studies. The experiments show that this new approach runs faster and scales better to larger, more complex specifications than related techniques.