Miracle-dz/UniFAR-FTUs huggingface dataset:
Surface-Adsorbed Contaminants Mediate the Importance of Chemotaxis and Haptotaxis for Bacterial Transport Through Soils

Chemotaxis and haptotaxis are important biological mechanisms that influence microbial movement toward concentrated chemoattractants in mobile liquids and along immobile surfaces, respectively. This study investigated their coupled effect, as induced by naphthalene (10 mg L−1), on the transport and retention of two pollutant-degrading bacteria, Pseudomonas fluorescens 5RL (Pf5RL) and Pseudomonas stutzeri DQ1 (PsDQ1), in quartz sand and natural soil. The results demonstrated that PsDQ1 was not chemotactic, whereas Pf5RL was chemotactic at 25°C but not at 4°C due to the restricted movement. In a quartz sand column, haptotaxis did not play a role in increasing the transport of Pf5RL as compared with chemotaxis. Compared with a naphthalene-free soil column, Pf5RL broke through naphthalene-presaturated soil columns to reach a stable effluent concentration 0.5 pore volumes earlier due to advective chemotaxis occurring behind the plume front in the bulk solution. Pf5RL also demonstrated greater retention (e.g., a doubled rate of attachment and a one-third smaller breakthrough percentage) due to along-surface haptotaxis and near-surface chemotaxis occurring in less mobile water near the soil surface. However, both chemotaxis and haptotaxis were weakened when Pf5RL co-transported with naphthalene due to reduced adsorption of naphthalene on the soil. This study suggests that surface adsorption of naphthalene can mediate the relative importance of advective chemotaxis (facilitating initial breakthrough), near-surface chemotaxis (increasing bacterial collision), and haptotaxis (increasing bacterial residence time).
Ni(II) Interactions in Boreal Paenibacillus sp., Methylobacterium sp., Paraburkholderia sp., and Pseudomonas sp. Strains Isolated From an Acidic, Ombrotrophic Bog

The uptake of nickel [Ni(II)] by Paenibacillus sp. , Methylobacterium sp. , Paraburkholderia sp. , and Pseudomonas sp. strains isolated from a boreal bog was studied using batch experiments. All strains removed Ni(II) from the solution and the uptake efficiency was affected by the nutrient source, incubation temperature, time, and pH. As highest Ni uptake (with a maximum Kd of 1890 L/kg DW) was recorded for the Pseudomonas sp. strains, these bacteria were used in the following protein expression (SDS-PAGE and MALDI-TOFF), transmission electron microscopy (TEM) and EDS experiments. In addition, Freundlich and Langmuir sorption isotherms were determined. In the Ni(II) treated cells, dense crystalline intra-cellular accumulations were observed in TEM examinations, which were identified as Ni accumulations using EDS. SDS-PAGE and MALDI-TOFF spectra of Ni(II) treated cells showed several changes in the protein profiles, which can indicate active accumulation of Ni in these bacteria. Concurrently, we observed Ni(II) uptake to follow Freundlich and Langmuir isotherms, suggesting straight cellular biosorption in addition to the intra-cellular accumulation. The role of cellular (cell membrane and cell wall) functional groups involved in Ni(II) binding were therefore studied using Fourier transformation infrared spectroscopy. These analyses supported the potential role of the alcoholic hydroxyl, carboxyl and amine groups in Ni(II) binding in these bacteria, therefore suggesting two different Ni(II) uptake mechanisms; (i) intra-cellular accumulation [possibly connected to detoxification of Ni(II)], and (ii) straight biosorption on cell membrane/wall functional groups.
Whole Body Fuel Use: A Preliminary Study of Carbohydrate and Fat Oxidation During Water Exercise

Shallow water exercise (SWE) is a low-impact exercise due to the buoyancy effect (upward force) of water. Participants are typically immersed anywhere from waist to axillary level when performing SWE. One way of quantifying exercise intensity is to use rating of perceived exertion (RPE; Borg 6 to 20 Scale (7)). Very light efforts equate to a RPE of 9, somewhat hard equates to RPE-13, hard efforts are RPE-15, very hard efforts are RPE-17, while theoretical maximum is RPE-20. A unique aspect of the present study is that RPE was used by participants to self-regulate exercise intensity while performing SWE. This approach was deemed appropriate especially given that it is difficult to systematically control SWE intensity unlike regulating running speed during treadmill walking or jogging, or power output for a bicycle laboratory test (1). It is known that exercise intensity impacts energy expenditure and relative fuel (carbohydrate, fat) use. Most studies regarding energy expenditure and fuel use during human locomotion have examined land based exercises (4,8,9,10). A reason for this is that conducting physiological measurements while an individual is exercising on land is convenient, whereas conducting such assessments in water is difficult.
A Smoothed Algorithm with Convergence Analysis under Generalized Maximum Correntropy Criteria in Impulsive Interference

The generalized maximum correntropy criterion (GMCC) algorithm is computationally simple and robust against impulsive noise but it suffers from slow convergence speed as it is derived and based on stochastic gradient, which only use the current data sample. In order to deal with this issue, a smoothed GMCC algorithm (SGMCC) is proposed. In the SGMCC algorithm, instead of taking the exponential weighted average of gradient vector to approximate the expectation of the gradient vector, we take the exponential weighted average of the variable step-size so that the SGMCC algorithm can be viewed as a sign GMCC algorithm with smoothed variable step-size. Moreover, convergence performance analyses are derived in terms of variable step-size, mean-square stability and steady-state behavior to demonstrate the robustness of the proposed algorithm. At last, simulation comparisons show that the proposed algorithm is robust against impulsive noise and converges fast with lower computational complexity. Also, for the steady-state behavior, simulation results verify that the simulated value matches well with the theoretical one.
Phase 2 study of sunitinib in refractory thyroid cancer

6025 Background: Few treatment options exist for patients with refractory differentiated (including papillary, follicular, and Hurthle cell) and medullary thyroid cancers (DTC and MTC, respectively). Recent data suggest that thyroid cancers respond to antiangiogenic agents; in addition a subgroup of thyroid cancers harbor activating alterations in the RET gene. Sunitinib, has inhibitory activity against RET, VEGFR, and PDGFR, and thus has potential to be active in both DTC and MTC. Methods: Adult patients with DTC or MTC, refractory to curative treatment (surgery, external beam radiotherapy, or radioactive iodine (RAI) were required to have evidence of progressive disease within 6 months of study entry, ECOG performance status 0–2, and normal organ and bone marrow function. Treatment consisted of 6 week cycles of sunitinib malate 50 mg QD on a 4-week on/2-week off schedule. Primary endpoint was RECIST and biochemical response rate. Results: 43 subjects (37 DTC, 6 MTC) were enrolled; 25 male, 18 female; me.
Teaching Ordinal Patterns to a Computer: Efficient Encoding Algorithms Based on the Lehmer Code

Ordinal patterns are the common basis of various techniques used in the study of dynamical systems and nonlinear time series analysis. The present article focusses on the computational problem of turning time series into sequences of ordinal patterns. In a first step, a numerical encoding scheme for ordinal patterns is proposed. Utilising the classical Lehmer code, it enumerates ordinal patterns by consecutive non-negative integers, starting from zero. This compact representation considerably simplifies working with ordinal patterns in the digital domain. Subsequently, three algorithms for the efficient extraction of ordinal patterns from time series are discussed, including previously published approaches that can be adapted to the Lehmer code. The respective strengths and weaknesses of those algorithms are discussed, and further substantiated by benchmark results. One of the algorithms stands out in terms of scalability: its run-time increases linearly with both the pattern order and the sequence length, while its memory footprint is practically negligible. These properties enable the study of high-dimensional pattern spaces at low computational cost. In summary, the tools described herein may improve the efficiency of virtually any ordinal pattern-based analysis method, among them quantitative measures like permutation entropy and symbolic transfer entropy, but also techniques like forbidden pattern identification. Moreover, the concepts presented may allow for putting ideas into practice that up to now had been hindered by computational burden. To enable smooth evaluation, a function library written in the C programming language, as well as language bindings and native implementations for various numerical computation environments are provided in the supplements.
Biological Properties and Bioactive Components of Mentha spicata L. Essential Oil: Focus on Potential Benefits in the Treatment of Obesity, Alzheimer's Disease, Dermatophytosis, and Drug-Resistant Infections

In the present study, the medicinal aromatic plant Mentha spicata has been investigated as a source of essential oil (EO) and pharmaceuticals. The quantity and composition of EO from M. spicata cultivated in Palestine were analyzed seasonally over a three-year period. A significantly higher EO content was produced in summer and fall months (2.54–2.79%). Chemical analysis of EO revealed 31 compounds with oxygenated monoterpenes (90%) as the most abundant components followed by sesquiterpene and monoterpene hydrocarbons (6 and 3%, respectively). M spicata can be characterized as a carvone chemotype (65%). EO and carvone have shown strong inhibitory activities against the principal enzymes associated with Alzheimer's disease (AD) and overweight diseases (cholinesterase and porcine pancreatic lipase) and also shown strong antidermatophytic activity against Microsporum canis, Trichophyton rubrum, T. mentagrophytes, and Epidermophyton floccosum. The pancreatic lipase inhibition and the synergism showed the potential activity of M. spicata EO and carvone and that their combinations with standard drugs can be useful for the treatment of obesity and overweight. The results also demonstrated that, in addition to their significant inhibitory activity against biofilm formation of methicillin-resistant Staphylococcus aureus (MRSA), M. spicata EO and carvone had a strong inhibitory effect on metabolic activity and biomass of the preformed biofilm. The current study supports the utilization of M. spicata EO as a traditional medicine and opens perceptions to find more potent substances in the EO for the management of obesity, AD, and dermatophytosis and for combating drug-resistant bacterial infections.
E2F6 is essential for cell viability in breast cancer cells during replication stress

E2F6 is a member of the E2F family of transcription factors involved in regulation of a wide variety of genes through both activation and repression. E2F6 has been reported as overexpressed in breast cancers but whether or not this is important for tumor development is unclear. We first checked E2F6 expression in tumor cDNAs and the protein level in a range of breast cancer cell lines. RNA interference-mediated depletion was then used to assess the importance of E2F6 expression in cell lines with regard to cell cycle profile using fluorescence-activated cell sorting and a cell survival assay using (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). The overexpression of E2F6 was confirmed in breast tumor cDNA samples and breast cancer cell lines. Depletion of E2F6 in the breast cancer cells reduced cell viability in MCF-7, T-47D, and MDA-MB-231 cells. There was little effect in the nontumor breast cell line MCF-10A. The deleterious effect on cancer cells was greater during replication stress, leading to an increase in the proportion of breast cancer cells with sub-G1 DNA content. These results suggest that E2F6 might be essential for the survival of breast cancer cells experiencing replication stress, and therefore it could be a target for combined therapy.
Research Progress of the Functional Role of ACK1 in Breast Cancer

ACK1 is a nonreceptor tyrosine kinase with a unique structure, which is tightly related to the biological behavior of tumors. Previous studies have demonstrated that ACK1 was involved with multiple signaling pathways of tumor progression. Its crucial role in tumor cell proliferation, apoptosis, invasion, and metastasis was tightly related to the prognosis and clinicopathology of cancer. ACK1 has a unique way of regulating cellular pathways, different from other nonreceptor tyrosine kinases. As an oncogenic kinase, recent studies have shown that ACK1 plays a critical regulatory role in the initiation and progression of tumors. In this review, we will be summarizing the structural characteristics, activation, and regulation of ACK1 in breast cancer, aiming to deeply understand the functional and mechanistic role of ACK1 and provide novel therapeutic strategies for breast cancer treatment.
Kinematic Parameters for Tracking Patient Progress during Upper Limb Robot-Assisted Rehabilitation: An Observational Study on Subacute Stroke Subjects

Background Upper limb robot-assisted therapy (RT) provides intensive, repetitive, and task-specific treatment, and its efficacy for stroke survivors is well established in literature. Biomechanical data from robotic devices has been widely employed for patient's assessment, but rarely it has been analysed for tracking patient progress during RT. The goal of this retrospective study is to analyse built-in kinematic data registered by a planar end-effector robot for assessing the time course of motor recovery and patient's workspace exploration skills. A comparison of subjects having mild and severe motor impairment has been also conducted. For that purpose, kinematic data recorded by a planar end-effector robot have been processed for investigating how motor performance in executing point-to-point trajectories with different directions changes during RT. Methods Observational retrospective study of 68 subacute stroke patients who conducted 20 daily sessions of upper limb RT with the InMotion 2.0 (Bionik Laboratories, USA): planar point-to-point reaching tasks with an “assist as needed” strategy. The following kinematic parameters (KPs) were computed for each subject and for each point-to-point trajectory executed during RT: movement accuracy, movement speed, number of peak speed, and task completion time. The Wilcoxon signed-rank tests were used with clinical outcomes. the Friedman test and post hoc Conover's test (Bonferroni's correction) were applied to KPs. A secondary data analysis has been conducted by comparing patients having different severities of motor impairment. The level of significance was set at p value < 0.05. Results At the RT onset, the movements were less accurate and smoothed, and showed higher times of execution than those executed at the end of treatment. The analysis of the time course of KPs highlighted that RT seems to improve the motor function mainly in the first sessions of treatment: most KPs show significant intersession differences during the first 5/10 sessions. Afterwards, no further significant variations occurred. The ability to perform movements away from the body and from the hemiparetic side remains more challenging. The results obtained from the data stratification show significant differences between subjects with mild and severe motor impairment. Conclusion Significant improvements in motor performance were registered during the time course of upper limb RT in subacute stroke patients. The outcomes depend on movement direction and motor impairment and pave the way to optimize healthcare resources and to design patient-tailored rehabilitative protocols.
HuoXueTongFu Formula Alleviates Intraperitoneal Adhesion by Regulating Macrophage Polarization and the SOCS/JAK2/STAT/PPAR-γ Signalling Pathway

Intraperitoneal adhesion is a common complication after abdominal surgery, which seriously affects the quality of life of patients. HuoXueTongFu Formula (HXTF) plays an important role in the prevention and treatment of intraperitoneal adhesions. However, the molecular-related mechanisms are still not fully known. In this study, the model of Intrapetitoneal adhesion was established by cecum abrasion and treated with HXTF for one week. RAW264.7 cells were given LPS, IFN-γ, IL-4, HXTF-medicated serum, and PPAR-γ agonist/antagonist, respectively. Histopathology, flow cytometry, ELISA, real-time PCR, and Western blotting were used to further detect the related protein, M1/M2 polarization tendency, and PPAR-γ nuclear translocation. The deposition of collagen fibres reduced in the local area of rats after the operation with HXTF treatment. Similar to IL-4, HXTF induced a tendency for macrophages to polarize toward M2 and promoted peroxisome proliferator-activated receptor-gamma (PPAR-γ) nuclear translocation. Furthermore, the use of HXTF and PPAR-γ agonists downregulated macrophage M1 polarization-related factors IL-1, IL-6, and TNF-alpha and upregulated M2 polarization-related factors IL-4, IL-10, and TGF-beta 1. Meanwhile, the use of HXTF and PPAR-γ agonists downregulated the SOCS3/JAK2/STAT1 pathway and activated the SOCS1/STAT6/PPAR-γ pathway. These results show that HXTF may reduce intraperitoneal adhesion by inducing macrophage M2 polarization and regulating the SOCS/JAK2/STAT/PPAR-γ pathway.
Premature mortality attributable to smoking among Tunisian men in 2009

INTRODUCTION Tobacco smoking is a significant public health threat in the world, a risk factor for many diseases, and has been increasing in prevalence in many developing countries. In this study, we aimed to estimate the burden of premature deaths attributable to smoking among Tunisian men aged 35–69 years in 2009. METHODS The number of deaths attributable to smoking was estimated using the population attributable risk fraction method. Smoking prevalence was obtained from a nationally representative survey. Causes of death were obtained from the registry of the National Public Health Institute. Relative risks were taken from the American Cancer Society Prevention Study (CPS-II). RESULTS Total estimated premature deaths attributable to smoking among men in Tunisia were 2601 (95% CI: 2268–2877), accounting for 25% (95% CI: 23.3–26.6) of total male adult mortality. Cancer, cardiovascular and respiratory diseases were the major causes of premature deaths attributable to smoking with 1272 (95% CI: 1188–1329), 966 (95% CI: 779–1133) and 364 (300–415) deaths, respectively. CONCLUSIONS Tobacco smoking is highly relevant and is related to substantial premature mortality in Tunisia, around double that estimated for the region as a whole. This also has not decreased over the past 20 years. Urgent actions are needed to reduce this pandemic.
Systematic exploration of predicted destabilizing nonsynonymous single nucleotide polymorphisms (nsSNPs) of human aldehyde oxidase: A Bio‐informatics study

Aldehyde Oxidase (hAOX1) is a cytosolic enzyme involved in the metabolism of drugs and xenobiotic compounds. The enzyme belongs to the xanthine oxidase (XO) family of Mo containing enzyme and is a homo‐dimer of two 150 kDa monomers. Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs) of hAOX1 have been reported as affecting the ability of the enzyme to metabolize different substrates. Some of these nsSNPs have been biochemically and structurally characterized but the lack of a systematic and comprehensive study regarding all described and validated nsSNPs is urgent, due to the increasing importance of the enzyme in drug development, personalized medicine and therapy, as well as in pharmacogenetic studies. The objective of the present work was to collect all described nsSNPs of hAOX1 and utilize a series of bioinformatics tools to predict their effect on protein structure stability with putative implications on phenotypic functional consequences. Of 526 nsSNPs reported in NCBI‐dbSNP, 119 are identified as deleterious whereas 92 are identified as nondeleterious variants. The stability analysis was performed for 119 deleterious variants and the results suggest that 104 nsSNPs may be responsible for destabilizing the protein structure, whereas five variants may increase the protein stability. Four nsSNPs do not have any impact on protein structure (neutral nsSNPs) of hAOX1. The prediction results of the remaining six nsSNPs are nonconclusive. The in silico results were compared with available experimental data. This methodology can also be used to identify and prioritize the stabilizing and destabilizing variants in other enzymes involved in drug metabolism.
Diagnostic Value of Urine Cytology in 236 cases; a Comparison of Liquid-Based Preparation and Conventional Cytospin Method

Urine cytology is an important screening tool for urinary tract neoplasms. Liquid-based preparation methods, such as , have been introduced for non-gynecological samples. We aimed to assess the diagnostic accuracy of liquid-based preparations in urine cytology by comparing the results of the conventional Cytospin preparation method for the same samples. A total of 236 cases subject to urine cytology were enrolled in this study from January 2005 to December 2005. All cases were subjected to cystoscopy and if a malignancy was suspected, a biopsy was performed. Urine cytology slides were made using the preparation method and the conventional Cytospin and/or direct smear method from the individual samples. The results of urine cytology were compared with the final cystoscopic or histological diagnoses. We analyzed the sensitivity, specificity, positive predictive value, negative predictive value and accuracy of both cytology preparation methods. A total of 236 slides made using the liquid based method were satisfactory for slide quality, whereas 5 slides (2.1%) prepared by conventional methods were unsatisfactory because of air-drying, a thick smear, or a bloody or inflammatory background. The method showed 53.1% sensitivity, 92.6% specificity, a 92,6% positive predictive value, a 94.1% negative predictive value and 85,6% accuracy, while the conventional method showed 51% sensitivity, 98.4% specificity, a 92.6% positive predictive value, a 98.4% negative predictive value and 88,6% accuracy. Although the diagnostic values were equivalent between the use of the two methods, the quality of the cytology slides and the time consumed during the microscopic examination for a diagnosis were superior for the method than for the conventional method. In conclusion, our limited studies have shown that the use of the liquid based preparation method is beneficial to improve the quality of slides and reduce the duration for a microscopic examination, but did not show better sensitivity, accuracy and predictive values.
Programming a spatial water model for improving water efficiency in China

This paper deals with heavy pressures to save water in natural resource management due to increased water scarcity. We take the example of a Chinese watershed and investigate the water use efficiency in Chinese irrigated agriculture through a field study as dependent on investments in on-farm water saving technologies and canal water conveyance. The economic and environmental impacts of farmers adopting modern irrigation technologies and public sectors improving water transit systems are studied in particular. A spatial mathematical programming model is employed for optimization. The emphasis is on private and public investments in water saving. Water saving in a canal system enables an extension of the system and provides food and income for more farmers. The model results are of great value for policy makers and project managers, who want to optimize irrigation projects, because scenarios (for instance water and product pricing) are provided. We also provide references for farmers in applying suitable irrigation technologies.