Miracle-dz/UniFAR-FTUs huggingface dataset:
Short-term acute exposure to wildfire smoke and lung function in a Royal Canadian Mounted Police (RCMP) cohort

Rationale: The increasing incidence of extreme wildfire is becoming a concern for public health. Although long-term exposure to wildfire smoke is associated with respiratory illnesses, reports on the association between short-term occupational exposure to wildfire smoke and lung function remain scarce. Methods: In this cross-sectional study, we analyzed data of 218 Royal Canadian Mounted Police officers (mean age: 38{+/-}9 years) deployed at the Fort McMurray wildfire in 2016. Individual exposure to air pollutants was calculated by integrating the duration of exposure with the air quality parameters obtained from the nearest air quality monitoring station during the phase of deployment. Lung function was measured using spirometry and body plethysmography. Association between exposure and lung function was examined using principal component linear regression analysis, adjusting for potential confounders. Results: The participants were predominantly male (71%). Mean forced expiratory volume in 1 second (FEV1), and residual volume (RV) were 76.5{+/-}5.9 and 80.1{+/-}19.5 of % predicted. A marginal association was observed between the principal air pollution component and higher RV [{beta}: 1.55; 95%CI: -0.28 to 3.37 per interquartile range change of air pollution index], but not with other lung function indices. The association was significantly higher in participants who were screened within the first three months of deployment [2.80; 0.91 to 4.70] than those screened later [-0.28; -2.58 to 2.03], indicating a more acute effect of air pollution on peripheral airways. Conclusion: Acute short-term exposure to wildfire-associated air pollutants may impose subtle but clinically important deleterious respiratory effects, particularly in the peripheral airways.
Differentiation of human induced pluripotent or embryonic stem cells decreases the DNA damage response

Genomic integrity is critical for preservation of stem cell function and is, maintained through a robust DNA damage response (DDR) with systemized DNA DSB repair by either the non-homologous end joining (NHEJ) pathway or the homologous recombination (HR) pathway. To examine DDR during stem cell differentiation, human embryonic (hES) and induced pluripotent stem (IPS) cells were exposed to DNA damaging agents and DNA damage signaling/repair measured. Differentiated cells displayed a higher frequency of residual DNA damage, chromosomal aberrations, cells with delayed γ-H2AX foci disappearance and a reduced number of RAD51 foci. Factors impacting DNA DSB repair by HR formed reduced foci in differentiated cells. The reduction in repairosome foci formation after DNA damage was not due to changes in HR protein levels, which were unchanged by differentiation. Differentiated cells also displayed a higher frequency of stalled DNA replication forks and decreased firing of new replication origins from transient inhibition of DNA synthesis by hydroxyurea treatment. In addition, we observed that differentiated cells exhibit a higher frequency of R-loops. A similar decline in DDR was observed as early stage mouse astrocytes differentiated into later stage astrocytes. Our studies thus suggest that DSB repair by homologous recombination is increasingly impaired during stem cell differentiation while the NHEJ pathway is minimally altered.
Digestion of Insoluble Fluorides in Geochemical Samples by Ammonium Fluoride

The ability of ammonium fluoride attacking insoluble fluorides was studied. Ammonium fluoride was used to digest some geochemical certified reference materials instead of hydrofluoric acid. Inductively coupled plasma optical emission spectrometry and inductively coupled plasma mass spectrometry were employed to determined major, minor, and trace elements, respectively. By testing CRMs and a large number of real samples, it was determined that the effects on those elements, which easily formed insoluble fluorides, were better by ammonium fluoride than by hydrofluoric acid. Furthermore, it was more secure for operators using ammonium fluoride than hydrofluoric acid. A possible mechanism was also proposed.
A Lifetime Maximization Relay Selection Scheme in Wireless Body Area Networks.

Network Lifetime is one of the most important metrics in Wireless Body Area Networks (WBANs). In this paper, a relay selection scheme is proposed under the topology constrains specified in the IEEE 802.15. 6 standard to maximize the lifetime of WBANs through formulating and solving an optimization problem where relay selection of each node acts as optimization variable. Considering the diversity of the sensor nodes in WBANs, the optimization problem takes not only energy consumption rate but also energy difference among sensor nodes into account to improve the network lifetime performance. Since it is Non-deterministic Polynomial-hard (NP-hard) and intractable, a heuristic solution is then designed to rapidly address the optimization. The simulation results indicate that the proposed relay selection scheme has better performance in network lifetime compared with existing algorithms and that the heuristic solution has low time complexity with only a negligible performance degradation gap from optimal value. Furthermore, we also conduct simulations based on a general WBAN model to comprehensively illustrate the advantages of the proposed algorithm. At the end of the evaluation, we validate the feasibility of our proposed scheme via an implementation discussion.
Effects of Energetic Disorder and Mobility Anisotropy on Geminate Electron-hole Recombination in the Presence of a Donor-Acceptor Heterojunction †

Geminate electron-hole recombination in organic solids in the presence of a donor-acceptor heterojunction is studied by computer simulations. We analyze how the charge-pair separation probability in such systems is affected by energetic disorder of the media, anisotropy of charge-carrier mobilities, and other factors. We show that in energetically disordered systems the effect of heterojunction on the charge-pair separation probability is stronger than that in idealized systems without disorder. We also show that a mismatch between electron and hole mobilities reduces the separation probability, although in energetically disordered systems this effect is weaker compared to the case of no energetic disorder. We demonstrate that the most important factor that determines the charge-pair separation probability is the ratio of the sum of electron and hole mobilities to the rate constant of recombination reaction. We also consider systems with mobility anisotropy and calculate the electric field dependence of the charge-pair separation probability for all possible orientations of high-mobility axes in the donor and acceptor phases. We theoretically show that it is possible to increase the charge-pair separation probability by controlling the mobility anisotropy in heterojunction systems and in consequence to achieve higher efficiencies of organic photovoltaic devices.
Mechanism of precipitate formation during spontaneous crystallization from supersaturated aqueous solutions

The models of formation of salt precipitates during crystallization from supersaturated aqueous solutions are analyzed. The results of theoretical simulations and experimental studies are compared. The attention is focused on the processes of crystal aggregation and agglomeration. The data on the mechanism of crystal intergrowth under conditions of mass crystallization of salts from supersaturated aqueous solutions are considered. The intergrowth process is shown to be described most reliably by the model based on the Polak theory according to which in supersaturated solutions, connecting nucleus-bridges are formed within aggregates between the closest faces of neighbouring crystals. The bibliography includes 159 references.
A Seven Month Survey for the Detection of E. coli O157:H7 from Ground Beef Samples in the Markets of Turkey

A seven month period from the beginning October to the end of April 2004, a total of 126 ground beef samples were analyzed to determine the incidence of Escherichia coli (E. coli) O157:H7. Among the sampling months, the incidence of EHEC serotypes were only observed in April. Of the 126 ground beef samples, only one ground beef sample was positive for E. coli O157:H7, having a prevalence of 0.79 %. Five samples were found positive for E. coli O157 serotype, having a prevalence of 3.96 %. The results of this study reveal that the occurrence of EHEC serotypes in ground beef in the Kars (Eastern Turkey) seem to be seasonal and the level of E. coli O157 was significantly higher as compared to other studies in Turkey, but it is similar to studies performed in many countries around the world. Of the tested eighteen antibiotics, resistance towards three or more antibiotics were observed among the all isolates.
Safety and immunogenicity of a glycoprotein E gene-deleted bovine herpesvirus 1 strain as a candidate vaccine strain

A glycoprotein E-deleted Brazilian bovine herpesvirus 1 (BoHV-1gE;) was tested regarding to safety and immunogenicity. Intramuscular inoculation of young calves with a high virus dose did not result in clinical signs or virus shedding during acute infection or after dexamethasone administration. Calves vaccinated once IM (group I) or subcutaneously (group II) with live BoHV-1gE; or twice with inactivated virus plus aluminum hydroxide (group IV) or Montanide2; (group V) developed VN titers of 2 to 8 (GMT:2); 2 to 4 (GMT:1.65); 2 to 16 (GMT:2.45) and 2 to 128 (GMT:3.9), respectively. All BoHV-1gE; vaccinated calves remained negative in an anti-gE ELISA. Lastly, six young calves vaccinated with live BoHV-1gE; and subsequently challenged with a virulent BoHV-1 strain shed less virus and developed only mild and transient nasal signs comparing to unvaccinated calves. Thus, the recombinant BoHV-1gE; is safe and immunogenic for calves and allows for serological differentiation by a gE-ELISA test.
Nonlinear transformations for parameter estimation

On effectue des transformations non lineaires dans l'estimation de parametres d'apres le modele des moindres carres, dans le cas d'une variable. On evalue une methode de comparaison de differentes transformations et on se sert de mesures de non-linearite. Des methodes numeriques sont presentees pour reduire les effets de courbure
Fast and Efficient Removal of Cationic Dyes From Aqueous Solution by Collagen-Based Hydrogel Nanocomposites

A series of collagen-based hydrogel nanocomposites were prepared and applied as dye adsorbents. The certain variables affecting the dye adsorption such as initial concentration of dye solution, pH value, contact time and montmorilonite content were investigated to achieve maximum removal of Methylene Green (MG) and Crystal Violet (CV) from aqueous solutions. The experimental data showed that more than 90% of the maximum adsorption capacities of the optimized sample for MG and CV were achieved within the initial 10 min. Three isotherm models were carried out to describe adsorption capacity of the adsorbents.
EXTRACTION OF SNAKEHEAD FISH [Ophiocephalus striatus (Bloch, 1793)] INTO FISH PROTEIN CONCENTRATE AS ALBUMIN SOURCE USING VARIOUS SOLVENT

Study aimed to determine the optimum solvent for extraction of soluble protein (albumin) and identify the chemical composition of snakehead fish protein concentrate. The method was experimental while the treatments were the variation of solvents: distilled water, HCl 0.1 M, and NaCl 0.9 %. Soluble protein (albumin) and yield parameters analyzed by using completely randomized design (CRD) which consist three treatments and four replications, the other parameters were described descriptively. The result showed that the highest soluble protein (albumin) (7.65 %) was produced by HCl 0.1 M solvent with 2.55 % yield, 10.76 % dry basis moisture content, 63.78 % total protein content, and 2.54 % fat content.
Altered Indoleamine 2,3-Dioxygenase Production and Its Association to Inflammatory Cytokines in Peripheral Blood Mononuclear Cells Culture of Type 2 Diabetes Mellitus

Aim: To analyze indoleamine 2,3-dioxygenase (IDO) production in the cell culture supernatant of phytohemagglutinin (PHA)-stimulated peripheral blood mononuclear cells (PBMCs) from type 2 DM (T2DM) patients and investigate IDO’s association to pro- and anti-inflammatory cytokines. Subjects and methods: PBMC samples were collected from 21 T2DM patients and 17 normoglycemic participants, then stimulated with PHA for 3 days. Cytokine and IDO concentrations were measured in the PBMC culture supernatants. In vitro production of TNF-α, IL-6, interferon-γ, and IL-10 were measured using multiplex immunoassay. IDO concentration was assessed using ELISA. To assess how PHA stimulation altered IDO production and to minimize the unstimulated baseline effect of T2DM, we subtracted the PHA-stimulated IDO concentration from the unstimulated one. IBM SPSS version 23 was used for statistical analysis. Results: The IDO concentrations in the PBMC culture supernatants were significantly higher in T2DM patients regardless of whether they were unstimulated (P < .001) or PHA-stimulated (P = .012). Reduced IDO production was observed in 52.8% of T2DM patients and was associated with older age and lower interferon-γ levels. Conversely, 42.8% of T2DM patients showed increased IDO concentrations, which were correlated with the IL-6/IL-10 ratio (r = 0.683, P = .021) and interferon-γ/IL-10 ratio (r = 0.517, P = .077). Conclusion: The interferon-γ level was reduced in the PBMC culture supernatant of T2DM patients with reduced IDO production. Reduced IDO production in T2DM patients following PHA stimulation was associated with older age and, notably, higher baseline IDO concentrations. Since IDO is primarily produced by dendritic cells, reduced IDO production after PHA stimulation may indicate dendritic cell dysfunction.
Is Dynesys dynamic stabilization system superior to posterior lumbar fusion in the treatment of lumbar degenerative diseases?

Dynesys, a pedicle-based dynamic stabilization system, was introduced to overcome some undesirable complications of fusion procedures. Nevertheless, the theoretical advantages of Dynesys over fusion have not been clearly confirmed. The purpose of this editorial was to compare clinical and radiological outcomes of patients who underwent Dynesys system with those who underwent posterior lumbar fusion according to the existing literature and to see if the application of the Dynesys system is superior to the traditional lumbar fusion surgery. According to published clinical reports, the short-term effects of the Dynesys dynamic stabilization system are similar to that of traditional lumbar fusion surgery. Three comparative studies of Dynesys dynamic stabilization and fusion surgery with medium-term follow-up are encouraging. However, the results from four single-treatment-arm and small-sample studies of case series with long-term follow-up were not encouraging. In the present circumstances, it is not possible to conclude that the Dynesys dynamic stabilization system is superior to fusion surgery for lumbar degenerative diseases.
Pharmacological inhibition of syntenin PDZ2 domain impairs breast cancer cell activities and exosome loading with syndecan and EpCAM cargo

Abstract Exosomes support cell‐to‐cell communication in physiology and disease, including cancer. We currently lack tools, such as small chemicals, capable of modifying exosome composition and activity in a specific manner. Building on our previous understanding of how syntenin, and its PDZ partner syndecan (SDC), impact on exosome composition we optimized a small chemical compound targeting the PDZ2 domain of syntenin. In vitro , in tests on MCF‐7 breast carcinoma cells, this compound is non‐toxic and impairs cell proliferation, migration and primary sphere formation. It does not affect the size or the number of secreted particles, yet it decreases the amounts of exosomal syntenin, ALIX and SDC4 while leaving other exosomal markers unaffected. Interestingly, it also blocks the sorting of EpCAM, a bona fide target used for carcinoma exosome immunocapture. Our study highlights the first characterization of a small pharmacological inhibitor of the syntenin‐exosomal pathway, of potential interest for exosome research and oncology.
Hemorrhagic corpus luteum: Clinical management update

Hemorrhagic corpus luteum (HCL) is an ovarian cyst formed after ovulation and caused by spontaneous bleeding into a corpus luteum (CL) cyst. When HCL rupture happens, a hemoperitoneum results. Clinical symptoms are mainly due to peritoneal irritation by the blood effusion. The differential diagnosis is extensive and standard management is not defined. The authors elaborated a comparison of the differential diagnosis and therapeutic modalities from the laparoscopic approach to nonsurgical, medical options because hemorrhage from HCL is often self-limiting. The authors reviewed all data implicated with the development of HCL, trying to give homogeneity to literature data. The authors analyzed extensive literature data and subdivided the medical approach into many topics. The wait-and-see attitude avoids unnecessary laparoscopic surgery using supportive therapies (antifibrinolytic, analgesics, liquid infusion, transfusions and antibiotic prophylaxis). Surgical therapy: operative management should be laparoscopic, with surgical options such as luteumectomy, ovarian wedge-shaped excision or oophorectomy. Prevention: the possibility to preserve fertility is essential, mainly in patients with bleeding disorders or undergoing anticoagulant therapy; therefore, they need estro-progestinics or GnRH analogues to prevent ovulation and avoid further episodes of HCL. This review will aid physicians in making an early diagnosis of HCL, to avoid unnecessary surgery, and use the most effective treatment.
Safety and tolerability of GRF6019 in mild‐to‐moderate Alzheimer's disease dementia

Abstract Introduction This phase 2 trial evaluated the safety, tolerability, and feasibility of repeated infusions of the plasma fraction GRF6019 in mild‐to‐moderate Alzheimer's disease. Methods In this randomized, double‐blind, dose‐comparison trial, 47 patients were randomized 1:1 to receive daily infusions of 100 mL (n = 24) or 250 mL (n = 23) of GRF6019 for 5 consecutive days over two dosing periods separated by a treatment‐free interval of 3 months. Results The mean (standard deviation [SD]) age of the enrolled patients was 74.3 (6.9), and 62% were women. Most adverse events (55%) were mild, with no clinically significant differences in safety or tolerability between the two dose levels. The mean (SD) baseline Mini‐Mental State Examination score was 20.6 (3.7) in the 100 mL group and 19.6 (3.7) in the 250 mL group; at 24 weeks, the within‐patient mean change from baseline was –1.0 points (95% confidence interval [CI], –3.1 to 1.1) in the 100 mL group and +1.5 points (95% CI, –0.4 to 3.3) in the 250 mL group. The within‐patient mean change from baseline on the Alzheimer's Disease Assessment Scale‐Cognitive subscale was –0.4 points (95% CI, –2.9 to 2.2) in the 100 mL group, while in the 250 mL group it was –0.9 points (95% CI, –3.0 to 1.2). The within‐patient mean change from baseline on the Alzheimer's Disease Cooperative Study‐Activities of Daily Living was –0.7 points in the 100 mL group (95% CI, –4.3 to 3.0) and –1.3 points (95% CI, –3.4 to 0.7) in the 250 mL group. The mean change from baseline on the Category Fluency Test, Clinical Dementia Rating Scale–Sum of Boxes, Alzheimer's Disease Cooperative Study–Clinical Global Impression of Change, and Neuropsychiatric Inventory Questionnaire was similar for both treatment groups and did not show any worsening. Discussion GRF6019 was safe and well tolerated, and patients experienced no cognitive decline and minimal functional decline. These results support further development of GRF6019.
Atomic Layer Deposition of TiO2 Thin Films on the Inner Walls of Steel Tubes Increases Anti-coking Properties

To suppress catalytic coking, TiO2 passivation films were deposited on the inner walls of SS316 stainless steel tubes by atomic layer deposition (ALD). Indentation test results showed a platform on the indentation curve of TiO2 films grown over 2000 ALD cycles due to internal stress-induced microcracks. In coking experiments, the TiO2-coated tubes exhibited a higher heat flux and lower pressure difference than bare ones. Analysis of the coking surface revealed that TiO2 thin film passivation can reduce the size and number of particulate deposits. At the same time, passivation treatment inhibits the formation of filamentous carbon and improves anti-coking performance by reducing the ability of the tube to adsorb amorphous deposition products. The coking surfaces of TiO2-coated tubes had less graphitization, indicating that the coking products had fewer defects and lower activated carbon contents.
Wepy: A Flexible Software Framework for Simulating Rare Events with Weighted Ensemble Resampling

Here, we introduce the open-source software framework wepy (https://github.com/ADicksonLab/wepy) which is a toolkit for running and analyzing weighted ensemble (WE) simulations. The wepy toolkit is in pure Python and as such is highly portable and extensible, making it an excellent platform to develop and use new WE resampling algorithms such as WExplore, REVO, and others while leveraging the entire Python ecosystem. In addition, wepy simplifies WE-specific analyses by defining out-of-core tree-like data structures using the cross-platform HDF5 file format. In this paper, we discuss the motivations and challenges for simulating rare events in biomolecular systems. As has previously been shown, high-dimensional WE resampling algorithms such as WExplore and REVO have been successful at these tasks, especially for rare events that are difficult to describe by one or two collective variables. We explain in detail how wepy facilitates implementation of these algorithms, as well as aids in analyzing the unique structure of WE simulation results. To explain how wepy and WE work in general, we describe the mathematical formalism of WE, an overview of the architecture of wepy, and provide code examples of how to construct, run, and analyze simulation results for a protein–ligand system (T4 Lysozyme in an implicit solvent). This paper is written with a variety of readers in mind, including (1) those curious about how to leverage WE rare-event simulations for their domain, (2) current WE users who want to begin using new high-dimensional resamplers such as WExplore and REVO, and (3) expert users who would like to prototype or implement their own algorithms that can be easily adopted by others.