Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncoupling Charge Movement from Channel Opening in Voltage-gated Potassium Channels by Ruthenium Complexes*

The Kv2.1 channel generates a delayed-rectifier current in neurons and is responsible for modulation of neuronal spike frequency and membrane repolarization in pancreatic β-cells and cardiomyocytes. As with other tetrameric voltage-activated K+-channels, it has been proposed that each of the four Kv2.1 voltage-sensing domains activates independently upon depolarization, leading to a final concerted transition that causes channel opening. The mechanism by which voltage-sensor activation is coupled to the gating of the pore is still not understood. Here we show that the carbon-monoxide releasing molecule 2 (CORM-2) is an allosteric inhibitor of the Kv2.1 channel and that its inhibitory properties derive from the CORM-2 ability to largely reduce the voltage dependence of the opening transition, uncoupling voltage-sensor activation from the concerted opening transition. We additionally demonstrate that CORM-2 modulates Shaker K+-channels in a similar manner. Our data suggest that the mechanism of inhibition by CORM-2 may be common to voltage-activated channels and that this compound should be a useful tool for understanding the mechanisms of electromechanical coupling.
A new intelligent optimization technique for distribution systems reconfiguration

The loss minimization problem is one of the most important problems to save the operational cost in distribution systems. Therefore, more efficient approaches are required to handle such a combinatorial problem. This paper presents an efficient meta-heuristic method for reconfiguration of distribution systems. A Tabu Search (TS) algorithm is used to reconfigure distribution systems so that active power losses are globally minimized with turning on / off sectionalizing switches. TS algorithm is introduced with some modifications such as using a tabu list with variable size according to the system size; this should lead to robust algorithm, and prevent cycling. Also, a random multiplicative move is used in the search process to diversify the search toward unexplored regions. A new method to check the radial topology of the system is presented. The proposed method is applied to 32-node and 69-node distribution systems. The obtained results using the proposed TS approach are compared with results obtained using Simulated Annealing (SA) approach and Parallel Tabu Search (PTS) approach in the previous work to examine the performance.
Intubation and mechanical ventilation for COPD: development of an instrument to elicit patient preferences.

BACKGROUND Whether to simply provide palliative care or to intubate and use mechanical ventilation (MV) in a patient with severe COPD in acute respiratory failure is a difficult decision. The outcome of MV cannot be accurately predicted. Some patients cannot be weaned from the ventilator; those who are weaned often return to chronic severe respiratory disability. It is important that patients participate in this decision, but assistance is required. To address these issues, we developed and pilot-tested an aid to assist patients with MV decisions. METHODS A scenario-based decision aid was developed consisting of an audiocassette and a booklet describing intubation and MV and its possible outcomes. We used a probability tradeoff technique to elicit the patients' preferences and a decisional conflict scale to evaluate satisfaction. RESULTS With the assistance of the decision aid, all patients (10 men and 10 women) reached a decision. Two men and all 10 women declined MV. Mean decisional conflict was low (2.2 of a possible 5; SD, 0.9). At 1 year, only two patients (11%) had changed their decision. The agreement between physicians and patients was 65%; between next-of-kin and patients, there was uniform disagreement. CONCLUSION With the decision aid, stable decisions were made with satisfaction and confidence. Proxy decisions were incongruent, especially when made by family members. The strong gender effect should be further investigated. We suggest that the COPD decision aid be further tested in a community clinical setting.
Unique Features and Anti-microbial Targeting of Folate- and Flavin-Dependent Methyltransferases Required for Accurate Maintenance of Genetic Information

Comparative genome analyses have led to the discovery and characterization of novel flavin- and folate-dependent methyltransferases that mainly function in DNA precursor synthesis and post-transcriptional RNA modification by forming (ribo) thymidylate and its derivatives. Here we discuss the recent literature on the novel mechanistic features of these enzymes sometimes referred to as “uracil methyltransferases,” albeit we prefer to refer to them as (ribo) thymidylate synthases. These enzyme families attest to the convergent evolution of nucleic acid methylation. Special focus is given to describing the unique characteristics of these flavin- and folate-dependent enzymes that have emerged as new models for studying the non-canonical roles of reduced flavin co-factors (FADH2) in relaying carbon atoms between enzyme substrates. This ancient enzymatic methylation mechanism with a very wide phylogenetic distribution may be more commonly used for biological methylation reactions than previously anticipated. This notion is exemplified by the recent discovery of additional substrates for these enzymes. Moreover, similar reaction mechanisms can be reversed by demethylases, which remove methyl groups e.g., from human histones. Future work is now required to address whether the use of different methyl donors facilitates the regulation of distinct methylation reactions in the cell. It will also be of great interest to address whether the low activity flavin-dependent thymidylate synthases ThyX represent ancestral enzymes that were eventually replaced by the more active thymidylate synthases of the ThyA family to facilitate the maintenance of larger genomes in fast-growing microbes. Moreover, we discuss the recent efforts from several laboratories to identify selective anti-microbial compounds that target flavin-dependent thymidylate synthase ThyX. Altogether we underline how the discovery of the alternative flavoproteins required for methylation of DNA and/or RNA nucleotides, in addition to providing novel targets for antibiotics, has provided new insight into microbial physiology and virulence.
A phase II study of combined therapy with a BRAF inhibitor (vemurafenib) and interleukin-2 (aldesleukin) in patients with metastatic melanoma

ABSTRACT Background: Approximately 50% of melanomas harbor BRAF mutations. Treatment with BRAF +/− MEK inhibition is associated with favorable changes in the tumor microenvironment thus providing the rationale for combining targeted agents with immunotherapy. Methods: Patients with unresectable Stage III or IV BRAFV600E mutant melanoma were enrolled in a single-center prospective study (n = 6). Patients were eligible to receive two courses of HD-IL-2 and vemurafenib twice daily. The primary endpoint was progression-free survival (PFS) with secondary objectives including overall survival (OS), response rates (RR), and safety of combination therapy as compared to historical controls. Immune profiling was performed in longitudinal tissue samples, when available. Results: Overall RR was 83.3% (95% CI: 36%–99%) and 66.6% at 12 weeks. All patients eventually progressed, with three progressing on treatment and three progressing after the vemurafenib continuation phase ended. Median PFS was 35.8 weeks (95% CI: 16–57 weeks). Median OS was not reached; however, the time at which 75% of patients were still alive was 104.4 weeks. Change in circulating BRAFV600E levels correlated with response. Though combination therapy was associated with enhanced CD8 T cell infiltrate, an increase in regulatory T cell frequency was seen with HD-IL-2 administration, suggesting a potential limitation in this strategy. Conclusion: Combination vemurafenib and HD-IL-2 is well tolerated and associated with treatment responses. However, the HD-IL-2 induced increase in Tregs may abrogate potential synergy. Given the efficacy of regimens targeting the PD-1 pathway, strategies combining these regimens with BRAF-targeted therapy are currently underway, and the role of combination vemurafenib and HD-IL-2 is uncertain. Trial Registration: Clinical trial information: NCT01754376; https://clinicaltrials.gov/show/NCT01754376
Greening Reversed-Phase Liquid Chromatography Methods Using Alternative Solvents for Pharmaceutical Analysis

The greening of analytical methods has gained increasing interest in the field of pharmaceutical analysis to reduce environmental impacts and improve the health safety of analysts. Reversed-phase high-performance liquid chromatography (RP-HPLC) is the most widely used analytical technique involved in pharmaceutical drug development and manufacturing, such as the quality control of bulk drugs and pharmaceutical formulations, as well as the analysis of drugs in biological samples. However, RP-HPLC methods commonly use large amounts of organic solvents and generate high quantities of waste to be disposed, leading to some issues in terms of ecological impact and operator safety. In this context, greening HPLC methods is becoming highly desirable. One strategy to reduce the impact of hazardous solvents is to replace classically used organic solvents (i.e., acetonitrile and methanol) with greener ones. So far, ethanol has been the most often used alternative organic solvent. Others strategies have followed, such as the use of totally aqueous mobile phases, micellar liquid chromatography, and ionic liquids. These approaches have been well developed, as they do not require equipment investments and are rather economical. This review describes and critically discusses the recent advances in greening RP-HPLC methods dedicated to pharmaceutical analysis based on the use of alternative solvents.
External quality assessment in the measurement of haemoglobin by blood gas analysers in Belgium

Objective. The Belgian national External Quality Assessment Scheme (EQAS) for haematology organized a survey to assess the reliability of haemoglobin (Hb) measurements with the blood gas analysers (BGAs) currently available in Belgian hospitals. Material and methods. All hospital laboratories received two specimens of fresh EDTA anticoagulated whole blood and were asked to determine the Hb concentration using both the conventional haematology analyser (HA) and all BGAs in the hospital. Ninety‐seven hospital laboratories participated in the study and a total of 166 results were reported. The BGAs used (grouped according to technology) were Rapidlab 845, 855, 865 (Bayer 1, n = 41), Rapidlab 1245, 1265, Rapidpoint 405 (Bayer 2, n = 19), GEM Premier 3000 (Instrumentation Laboratory, IL, n = 13), ABL 500 and 600 series (Radiometer 1, n = 13), ABL 700 and 800 series (Radiometer 2, n = 35), Omni C, S5 (Roche 1, n = 7), Omni 3, 6, 9, S2, S4, S6 (Roche 2, n = 21). Results. For the BGAs from Bayer, Radiometer and Roche, interlaboratory variation ranged from 0.6 % to 4.1 %, indicating good precision and close agreement between centres. A significant negative bias observed on the GEM Premier 3000 using the EDTA anticoagulated blood samples did not appear to be present in fresh heparinized whole blood samples. There was no significant difference in imprecision and bias between Hb measurements on BGA situated in and outside the central laboratory.
Echinococcus granulosus cyst fluid enhances epithelial‐mesenchymal transition

Cystic echinococcosis is characterized by fluid‐filled hydatid cysts in the liver and lungs. The cysts are surrounded by a host fibrous layer (the pericyst) which acts to isolate the parasite from surrounding tissues. Previous studies in liver cysts have indicated that the parasite may be a stimulating fibrosis. The aim of this study was to investigate whether hydatid cyst fluid (HCF) could influence the potential for fibrosis to occur in lung tissue by stimulating epithelial to mesenchymal transition (EMT) in a human lung epithelial cell line. An adenocarcinoma‐derived alveolar basal epithelial cell line (A549) was used as a model for human alveolar epithelial cells (AEC II). These were cultured in vitro with HCF (UK sheep origin). Assays to investigate cell proliferation, cell migration and expression of cytoskeletal markers showed that HCF could stimulate changes indicative of EMT, including enhanced cell proliferation and migration; increased expression of mesenchymal cytoskeletal markers (fibronectin and vimentin) accompanied by a down‐regulation of an epithelial marker (E‐cadherin). Molecules within hydatid cyst fluid are capable of inducing phenotypic changes in A549 cells indicating that the parasite has the potential to modify lung epithelial cells which could contribute to fibrotic reactions.
Auditory stream segregation in monkey auditory cortex: effects of frequency separation, presentation rate, and tone duration.

Auditory stream segregation refers to the organization of sequential sounds into "perceptual streams" reflecting individual environmental sound sources. In the present study, sequences of alternating high and low tones, ". ABAB. ," similar to those used in psychoacoustic experiments on stream segregation, were presented to awake monkeys while neural activity was recorded in primary auditory cortex (A1). Tone frequency separation (AF), tone presentation rate (PR), and tone duration (TD) were systematically varied to examine whether neural responses correlate with effects of these variables on perceptual stream segregation. "A" tones were fixed at the best frequency of the recording site, while "B" tones were displaced in frequency from "A" tones by an amount = delta F. As PR increased, "B" tone responses decreased in amplitude to a greater extent than "A" tone responses, yielding neural response patterns dominated by "A" tone responses occurring at half the alternation rate. Increasing TD facilitated the differential attenuation of "B" tone responses. These findings parallel psychoacoustic data and suggest a physiological model of stream segregation whereby increasing delta F, PR, or TD enhances spatial differentiation of "A" tone and "B" tone responses along the tonotopic map in A1.
TorusE: Knowledge Graph Embedding on a Lie Group

Knowledge graphs are useful for many artificial intelligence (AI) tasks. However, knowledge graphs often have missing facts. To populate the graphs, knowledge graph embedding models have been developed. Knowledge graph embedding models map entities and relations in a knowledge graph to a vector space and predict unknown triples by scoring candidate triples. TransE is the first translation-based method and it is well known because of its simplicity and efficiency for knowledge graph completion. It employs the principle that the differences between entity embeddings represent their relations. The principle seems very simple, but it can effectively capture the rules of a knowledge graph. However, TransE has a problem with its regularization. TransE forces entity embeddings to be on a sphere in the embedding vector space. This regularization warps the embeddings and makes it difficult for them to fulfill the abovementioned principle. The regularization also affects adversely the accuracies of the link predictions. On the other hand, regularization is important because entity embeddings diverge by negative sampling without it. This paper proposes a novel embedding model, TorusE, to solve the regularization problem. The principle of TransE can be defined on any Lie group. A torus, which is one of the compact Lie groups, can be chosen for the embedding space to avoid regularization. To the best of our knowledge, TorusE is the first model that embeds objects on other than a real or complex vector space, and this paper is the first to formally discuss the problem of regularization of TransE. Our approach outperforms other state-of-the-art approaches such as TransE, DistMult and ComplEx on a standard link prediction task. We show that TorusE is scalable to large-size knowledge graphs and is faster than the original TransE.
Initial testing (stage 1) of the proteasome inhibitor bortezomib by the pediatric preclinical testing program

Bortezomib is a proteasome inhibitor that has been approved by FDA for the treatment of multiple myeloma and that has completed phase 1 testing in children. The purpose of the current study was to evaluate the antitumor activity of bortezomib against the in vitro and in vivo childhood cancer preclinical models of the Pediatric Preclinical Testing Program (PPTP).
Germ Cell and Dose-Dependent DNA Damage Measured by the Comet Assay in Murine Spermatozoaa after Testicular X-Irradiation1

Abstract The single-cell gel electrophoresis (Comet) assay has been widely used to measure DNA damage in human sperm in a variety of physiological and pathological conditions. We investigated the effects of in vivo radiation, a known genotoxin, on spermatogenic cells of the mouse testis and examined sperm collected from the vas deferens using the neutral Comet assay. Irradiation of differentiating spermatogonia with 0.25–4 Gy X-rays produced a dose-related increase in DNA damage in sperm collected 45 days later. Increases were found when measuring Comet tail length and percentage of tail DNA, but the greatest changes were in tail moment (a product of tail length and tail DNA). Spermatids, spermatocytes, differentiating spermatogonia, and stem cell spermatogonia were also irradiated in vivo with 4 Gy X-rays. DNA damage was indirectly deduced to occur at all stages. The maximum increase was seen in differentiating spermatogonia. DNA damaged cells were, surprisingly, still detected 120 days after stem cell spermatogonia had been irradiated. The distribution of DNA damage among individual sperm cells after irradiation was heterogeneous. This was seen most clearly when changes in the Comet tail length were measured when there were discrete undamaged and damaged populations. After increasing doses of irradiation, an increasing proportion of cells were found in the damaged population. Because a proportion of undamaged sperm cells remains after all but the highest dose, the possibility of normal fertility remains. However, fertilization with a spermatozoa carrying high amounts of DNA damage could lead to effects as diverse as embryonic death and cancer susceptibility in the offspring.
Observed Volatility in Effectiveness Metrics

Information retrieval research and commercial search system evaluation both rely heavily on the use of batch evaluation and numerical system comparisons using effectiveness metrics. Batch evaluation provides a relatively low-cost alternative to user studies, and permits repeatable and incrementally varying experimentation in research situations in which access to high-volume query/click streams is not possible. As a result, the IR community has invested considerable effort into formulating, justifying, comparing, and contrasting a large number of alternative metrics. In this paper we consider a very simple question: to what extent can the various metrics be said to give rise to stable scores; that is, evaluations in which the process of adding further relevance information creates refined score estimates rather than different score estimates. Underlying this question is a fundamental concern, namely, whether the numeric behavior of metrics provides confidence that comparative system evaluations based on the metrics are robust and defensible.
The feeding behavior of dairy cows: considerations to improve cow welfare and productivity.

One of the primary objectives of dairy producers is to promote dry matter intake (DMI) to support milk production. Considerable research to date has focused on improving the DMI of lactating dairy cows by changing the nutrient composition of feeds. However, the DMI of group-housed lactating dairy cows is also affected by feeding behavior, which is modulated by the environment, management, health, and social interactions. For example, management practices such as overcrowding at the feed bunk, and feeding and milking times and frequencies may affect dairy cow feeding behavior, and the social status of each cow may influence her ability to gain access to feed at the time when she wants to eat. The opportunity for high producing dairy cows to eat whenever they want is important to maintain cow health, welfare and productivity, and ultimately profitability of the farm. Therefore, dairy producers can use knowledge of animal behavior to improve cow welfare and performance.
On CD28/CD40 ligand costimulation, common gamma-chain signals, and the alloimmune response.

Activation and robust expansion of naive T cells often require T cell costimulatory signals and T cell growth factors. However, the precise growth and costimulation requirements for activation and expansion of CD4(+) and CD8(+) T cells in vivo in allograft response are still not clearly defined. In the present study, we critically examined the role of CD28/CD40 ligand (CD40L) costimulation and the common gamma-chain (gamma(c)) signals, a shared signaling component by receptors for all known T cell growth factors (i.e., IL-2, IL-4, IL-7, IL-9, IL-15, IL-21), in activation and expansion of CD4(+) and CD8(+) T cells in the allogeneic hosts. We found that CD28/CD40L costimulation and the gamma(c) signals are differentially involved in proliferation and clonal expansion of CD4(+) and CD8(+) T cells in response to alloantigen stimulation. CD8(+) T cells are highly dependent on the gamma(c) signals for survival, expansion, and functional maturation, whereas in vivo expansion of alloreactive CD4(+) T cells is largely gamma(c) independent. T cell costimulation via CD28 and CD40L, however, is necessary and sufficient for activation and expansion of CD4(+) T cells in vivo. In a skin transplant model, blocking both CD28/CD40L and the gamma(c) pathways induced prolonged skin allograft survival. Our study provides critical insights that the CD4 and CD8 compartments are most likely governed by distinct mechanisms in vivo, and targeting both costimulatory and gamma(c) signals may be highly effective in certain cytopathic conditions involving activation of both CD4(+) and CD8(+) T cells.
Use of hydroxy‐methyl‐glutaryl coenzyme A reductase inhibitors is associated with risk of lymphoid malignancies

It has been speculated that the use of hydroxy‐methyl‐glutaryl coenzyme A reductase inhibitors (statins) is associated with the risk of malignant diseases. Considering their immunosuppressive activities, malignant diseases that are associated with an immunosuppressive status seem feasible to examine the association. We therefore examined the association between statin use and development of lymphoid malignancies in a case‐control study. Cases were 221 consecutive incident cases with histopathologically proven lymphoid malignancies (lymphoma and myeloma), hospitalized in the Department of Hematology of Toranomon Hospital (Tokyo, Japan) between 1995 and 2001. Two independent control groups, comprising 442 and 437 inpatients without malignancies from the Departments of Orthopedics and Otorhinolaryngology of the same hospital, were selected to test for consistency of association. Controls were matched individually with cases for age, sex and year of admission. Subject information, including statin use, was abstracted from medical records at the time of hospitalization. Strength of association was evaluated as an adjusted odds ratios (aOR) using a conditional logistic regression model. A higher frequency of statin use was found among patients with lymphoid malignancies in comparison with both orthopedic (aOR 2.11, 95% CI 1.20–3.69, P = 0.009) and otorhinolaryngology patients (aOR 2.59, 95% CI 1.45–4.65, P = 0.001), the significance being maintained when the two control groups were combined (aOR 2.24, 95% CI 1.37–3.66, P = 0.001). In conclusion, we observed an elevated risk of lymphoid malignancy with statin use among Japanese patients. Further evaluations in different populations are required to draw conclusions as to the carcinogenicity of lymphoid malignancies with statin use. (Cancer Sci 2006; 97: 133 –138)