Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential effects of lipids and lyso-lipids on the mechanosensitivity of the mechanosensitive channels MscL and MscS

Mechanosensitive (MS) channels of small (MscS) and large (MscL) conductance are the major players in the protection of bacterial cells against hypoosmotic shock. Although a great deal is known about structure and function of these channels, much less is known about how membrane lipids may influence their mechanosensitivity and function. In this study, we use liposome coreconstitution to examine the effects of different types of lipids on MscS and MscL mechanosensitivity simultaneously using the patch-clamp technique and confocal microscopy. Fluorescence lifetime imaging (FLIM)-FRET microscopy demonstrated that coreconstitution of MscS and MscL led to clustering of these channels causing a significant increase in the MscS activation threshold. Furthermore, the MscL/MscS threshold ratio dramatically decreased in thinner compared with thicker bilayers and upon addition of cholesterol, known to affect the bilayer thickness, stiffness and pressure profile. In contrast, application of micromolar concentrations of lysophosphatidylcholine (LPC) led to an increase of the MscL/MscS threshold ratio. These data suggest that differences in hydrophobic mismatch and bilayer stiffness, change in transbilayer pressure profile, and close proximity of MscL and MscS affect the structural dynamics of both channels to a different extent. Our findings may have far-reaching implications for other types of ion channels and membrane proteins that, like MscL and MscS, may coexist in multiple molecular complexes and, consequently, have their activation characteristics significantly affected by changes in the lipid environment and their proximity to each other.
Insights into the physiomodulatory role of histaminergic receptors in vertebrate skin pigmentation

All organisms, from simple invertebrates to complex human beings, exist in different colors and patterns, which arise from unique distribution of pigments throughout the body. Being the largest organ of the body, skin is always under the influence of internal and external factors that often react to certain intrinsic agents in an unorthodox manner, modifying the integral pigmentation patterns and resulting into complex physiological aberrancies. One of these intrinsic agents involved in numerous immunological and non-immunological processes within the body is histamine. Histamine mediates its multifarious biological activities stimulated by various immunological and non-immunological stimuli via differential expression of its four classes of receptors (H1, H2, H3, and H4) on effector cells. Interestingly, recent studies have described the expression of functional histamine receptors in vertebrate pigment cells melanocytes, emphasizing the potential physiomodulatory effects of this molecule in the phenomenon of skin pigmentation. This noteworthy finding has opened numerous perspectives to elucidate several contentions regarding skin-related conditions. The focus of this review is to provide an updated overview of the involvement and role of histamine and its receptors together with the physiological and pharmacological aspects of their agonists and antagonists impinging the phenomenon of pigmentation and the mechanisms by which they do so.
Highly accurate diagnosis of cancer in thyroid nodules with follicular neoplasm/suspicious for a follicular neoplasm cytology by ThyroSeq v2 next‐generation sequencing assay

Fine‐needle aspiration (FNA) cytology is a common approach to evaluating thyroid nodules, although 20% to 30% of FNAs have indeterminate cytology, which hampers the appropriate management of these patients. Follicular (or oncocytic) neoplasm/suspicious for a follicular (or oncocytic) neoplasm (FN/SFN) is a common indeterminate diagnosis with a cancer risk of approximately 15% to 30%. In this study, the authors tested whether the most complete next‐generation sequencing (NGS) panel of genetic markers could significantly improve cancer diagnosis in these nodules.
Molecular Mechanisms for Species Differences in Organic Anion Transporter 1, OAT1: Implications for Renal Drug Toxicity

Species differences in renal drug transporters continue to plague drug development with animal models failing to adequately predict renal drug toxicity. For example, adefovir, a renally excreted antiviral drug, failed clinical studies for human immunodeficiency virus due to pronounced nephrotoxicity in humans. In this study, we demonstrated that there are large species differences in the kinetics of interactions of a key class of antiviral drugs, acyclic nucleoside phosphonates (ANPs), with organic anion transporter 1 [(OAT1) SLC22A6] and identified a key amino acid residue responsible for these differences. In OAT1 stably transfected human embryonic kidney 293 cells, the Km value of tenofovir for human OAT1 (hOAT1) was significantly lower than for OAT1 orthologs from common preclinical animals, including cynomolgus monkey, mouse, rat, and dog. Chimeric and site-directed mutagenesis studies along with comparative structure modeling identified serine at position 203 (S203) in hOAT1 as a determinant of its lower Km value. Furthermore, S203 is conserved in apes, and in contrast alanine at the equivalent position is conserved in preclinical animals and Old World monkeys, the most related primates to apes. Intriguingly, transport efficiencies are significantly higher for OAT1 orthologs from apes with high serum uric acid (SUA) levels than for the orthologs from species with low serum uric acid levels. In conclusion, our data provide a molecular mechanism underlying species differences in renal accumulation of nephrotoxic ANPs and a novel insight into OAT1 transport function in primate evolution.
The Effects of Variations in Percent of Naturally Occurring Complex and Simple Carbohydrates on Plasma Glucose and Insulin Response in Individuals with Non-insulin-dependent Diabetes Mellitus

In the present study, 12 patients with non-insulin-dependent diabetes mellitus (NIDDM) consumed eucaloric, mixed food diets on three consecutive days. Diets provided 50% of the calories as carbohydrate, 35% as fat, and 15% as protein. The percent of carbohydrate fed as complex (starches) and simple (monoand disaccharides) varied among the 3 days. On day 1, the diet contained 80% of the carbohydrate as complex and 20% as simple (80/20); another contained 50% complex and 50% simple (50/50); and the final diet contained 20% of the carbohydrate as complex and 80% as simple (20/80). All simple carbohydrates represent naturally occurring sugars in fruits, vegetables, and dairy products. No refined sugars were added to any of the diets. The three experimental diets were randomly assigned using a 3 × 3 Latin square design. Blood was obtained hourly from 0800 to 1700 h for day-long glucose and insulin concentrations, and 24-h urine collections were made for the measurement of urine glucose. Mean (± SEM) day-long glucose concentrations were significantly greater for the 80/20 diet (2245 ± 199 mg/dl · h, P < 0.05) than for either the 50/ 50 (2030 ± 157 mg/dl · h) or the 20/80 diets (2008 ± 160 mg/dl · h). No significant differences were noted between the 50/50 and the 20/80 diets. In contrast, day-long insulin concentrations were not significantly different with 401 ± 62, 370 ± 50, and 369 ± 60 μU/ ml · h on the 80/20, 50/50, and 20/80 diets, respectively. Twenty-four-hour urinary glucose excretion paralleled plasma glucose concentrations. Significant differences were noted when the 80/20 diet (25.1 ± 4.5 g/ 24 h, P < 0.05) was compared with the 20/80 diet (9.7 ± 3.3 g/24 h). Substantial quantitative differences also existed between the 80/20 and 50/50 (12.2 ± 4.5 g7sol;24 h), but these differences did not reach statistical significance. The results of the present study support the hypothesis that variations in relative proportions of naturally occurring, complex and simple dietary carbohydrate will have no deleterious effect on glycemia in patients with NIDDM. Thus, there seems to be no apparent reason why patients with NIDDM should avoid foods that are high in naturally occurring, simple carbohydrate.
Altered States of Telomere Deprotection and the Two-Stage Mechanism of Replicative Aging

ABSTRACT The molecular distinctions between mortality stages 1 (M1; senescence) and 2 (M2; crisis) of human replicative aging are ill defined. We demonstrate a qualitative difference between telomeric end associations at M1 and the end fusions that produce dicentric chromosomes and breakage-fusion cycles. Knockdown of ligase IV sufficient to completely inhibit radiation-induced dicentric chromosome formation had no effect on the frequency of telomere associations (TAs), establishing that TAs are not covalent conventional nonhomologous end-joining (NHEJ) products. TAs preceded and were more numerous than dicentric chromosomes. Cells initially tolerated dicentric chromosomes without dying, but eventually, a combination of too many TAs and dicentrics/complex chromosomal rearrangements resulted in apoptosis. We propose a working model in which end associations represent abortive DNA repair intermediates when the number of telomeric repeats is too small to completely inhibit DNA damage signaling but is sufficient to prevent the final covalent ligation step of NHEJ and induces the M1 checkpoint arrest in normal human cells. Rather than being all-or-none, telomere deprotection would thus proceed first through TAs before additional shortening leads to dicentric chromosomes. M2/crisis involves both qualitative changes (a shift from TAs to TAs plus dicentric chromosomes) and quantitative changes (an increase in the number of dysfunctional telomeres).
Human neutrophil elastase mediates fibrinolysis shutdown through competitive degradation of plasminogen and generation of angiostatin

BACKGROUND A subset of trauma patients undergo fibrinolysis shutdown rather than pathologic hyperfibrinolysis, contributing to organ failure. The molecular basis for fibrinolysis shutdown in trauma is incompletely understood. Elastase released from primed/activated human neutrophils (HNE) has historically been described as fibrin(ogen)olytic. However, HNE can also degrade plasminogen (PLG) to angiostatin (ANG), retaining the kringle domains but not the proteolytic function, and could thereby compete for generation of active plasmin by tissue plasminogen activator (tPA). We hypothesized that HNE can drive fibrinolysis shutdown rather than fibrinolysis. METHODS Turbidometry was performed using light scatter (&lgr; = 620 nm) in a purified fibrinogen + PLG system and in healthy citrate plasma clotted with Ca2+/thrombin ± tPA, ±HNE, and ±ANG to evaluate HNE effects on fibrinolysis, quantified by time to transition midpoint (Tm). &Dgr;Tm from control is reported as percent of control ±95% CI. Purified HNE coincubated with PLG or tPA was analyzed by western blot to identify cleavage products. Exogenous HNE was mixed ex vivo with healthy volunteer blood (n = 7) and used in TEG ± tPA to evaluate effects on fibrinolysis. RESULTS HNE did not cause measurable fibrinolysis on fibrin clots, clotted plasma, or whole blood as assessed by turbidometry or TEG in the absence of tPA. Upon tPA treatment, all three methods of evaluating fibrinolysis showed delays and decreases in fibrinolysis caused by HNE relative to control: fibrin clot turbidometry &Dgr;Tm = 110.7% (CI 105.0–116.5%), clotted citrate plasma (n = 6 healthy volunteers) &Dgr;Tm = 126.1% (CI 110.4–141.8%), and whole blood native TEG (n = 7 healthy volunteers) with &Dgr;LY30 = 28% (p = 0.043). Western blot analysis of HNE–PLG co-incubation confirmed that HNE generates angiostatin K1–3, and plasma turbidity assays treated with angiostatin K1–3 delayed fibrinolysis. CONCLUSION HNE degrades PLG and generates angiostatin K1–3, which predominates over HNE cleavage of fibrin(ogen). These findings suggest that neutrophil release of elastase may underlie trauma-induced fibrinolytic shutdown.
Physicochemical study of percutaneous absorption enhancement by dimethyl sulfoxide: kinetic and thermodynamic determinants of dimethyl sulfoxide mediated mass transfer of alkanols.

By first determining the thermodynamic activities and activity coefficients of methanol, 1-butanol and 1-octanol in binary dimethyl sulfoxide:water media, it has been possible to separate solubilizing (thermodynamic) effects of dimethyl sulfoxide from its kinetic (diffusive) influence as they relate to the skin permeation of these small, nonelectrolyte alkanols. This was done by normalizing the experimental permeability coefficients found with full-thickness hairless mouse skin membranes to unit activity in the vehicle. When the dimethyl sulfoxide media were placed on both sides of the skin sections in a two compartment diffusion cell, activity-adjusted permeability coefficients of the permeants were invariant to dimethyl sulfoxide concentrations of 50% strength. Thus, up to this concentration and in the absence of net solvent crosscurrents, the permeabilities of methanol, 1-butanol, and 1-octanol appear to be strictly determined by partitioning into the stratum corneum. However, when the dimethyl sulfoxide percentage strength was raised to greater than or equal to 75%, activity-adjusted permeability increased systematically and profoundly, indicating severe barrier impairment with increased diffusion across the horny layer (kinetic effect). When neat dimethyl sulfoxide was placed on both sides of the skin, the experimental permeability coefficients of the three alcohols were maximal and equal in magnitude, suggesting total functional impairment of the stratum corneum. When the dimethyl sulfoxide media were placed in contact with the stratum corneum surface of the skin membranes only, accelerating effects were noted at dimethyl sulfoxide concentrations less than 50%, further supporting the idea that solvent cross flows themselves disrupt the horny structure. The degree of impairment was quantified under all experimental circumstances. (ABSTRACT TRUNCATED AT 250 WORDS)
The size of the last merger and time reversal in $\Lambda$-coalescents

Author(s): Kersting, Goetz; Schweinsberg, Jason; Wakolbinger, Anton | Abstract: We consider the number of blocks involved in the last merger of a $\Lambda$-coalescent started with $n$ blocks. We give conditions under which, as $n \to \infty$, the sequence of these random variables a) is tight, b) converges in distribution to a finite random variable or c) converges to infinity in probability. Our conditions are optimal for $\Lambda$-coalescents that have a dust component. For general $\Lambda$, we relate the three cases to the existence, uniqueness and non-existence of quasi-invariant measures for the dynamics of the block-counting process, and in case b) investigate the time-reversal of the block-counting process back from the time of the last merger.
Dengue Virus Modulates the Unfolded Protein Response in a Time-dependent Manner*

Flaviviruses, such as dengue virus (DENV), depend on the host endoplasmic reticulum for translation, replication, and packaging of their genomes. Here we report that DENV-2 infection modulates the unfolded protein response in a time-dependent manner. We show that early DENV-2 infection triggers and then suppresses PERK-mediated eIF2α phosphorylation and that in mid and late DENV-2 infection, the IRE1-XBP1 and ATF6 pathways are activated, respectively. Activation of IRE1-XBP1 correlated with induction of downstream targets GRP78, CHOP, and GADD34. Furthermore, induction of CHOP did not induce apoptotic markers, such as suppression of anti-apoptotic protein Bcl-2, activation of caspase-9 or caspase-3, and cleavage of poly(ADP-ribose) polymerase. Finally, we show that DENV-2 replication is affected in PERK−/− and IRE1−/− mouse embryo fibroblasts when compared with wild-type mouse embryo fibroblasts. These results demonstrate that time-dependent activation of the unfolded protein response by DENV-2 can override inhibition of translation, prevent apoptosis, and prolong the viral life cycle.
Assessment of Long-term Omalizumab Treatment in Patients with Severe Allergic Asthma Long-term Omalizumab Treatment in Severe Asthma

Objective. Several clinical studies have demonstrated the effectiveness of omalizumab in patients with severe allergic asthma but the treatment period has always been relatively short (4–12 months). In the literature, there are a few data about the long-term omalizumab therapy. We aimed to assess the long-term clinical and functional effectiveness of omalizumab treatment in severe allergic asthmatic patients, Methods. Medical records describing the patients’ status before the start of treatment, and also having been registered at the end of 4th, 12th, and 36th months from the commencement of treatment, and at the last visit where the patient was evaluated were used for omalizumab effectiveness assessments. Twenty-six patients (female/male: 21/5) with severe allergic asthma, uncontrolled despite GINA 2006 Step 4 therapy, were included in the study. Effectiveness outcomes included spirometry measurements, level of asthma control measured by asthma control test (ACT), systemic glucocorticosteroid (sGCS) use, emergency room (ER) visits, and hospitalizations for severe exacerbations. In addition, the quality of life was assessed using the quality of life questionnaire AQLQ(S) before, 4, and 36 months after treatment, Results. The mean age was 47.6 ± 13.9 and duration of allergic asthma was 22.7 ± 10.1 years. Serum total IgE levels were 322.0 ± 178.1 IU/mL. Mean duration of omalizumab treatment was 40.81 ± 8.2 months. FEV1 improved significantly at all control points versus baseline (p < .05). The level of asthma control as evaluated by ACT improved significantly after treatment (p < .05). We determined significantly reduced numbers of exacerbation, emergency visits, hospitalizations, sGCS, and SABA use by the end of 36 months (p < .05). The proportion of patients with improvements larger than 1.5 points in AQLQ(S) total score was 80.7% at the 4th month and 96.1% at the 36th month of treatment, Conclusions. This study showed that long-term therapy with omalizumab for up to 3 years was well tolerated with significant improvement both in symptoms and lung functions. Accordingly, long-term omalizumab treatment may be recommended for responders.
Bayesian penalized log-likelihood ratio approach for dose response clinical trial studies

ABSTRACT In literature, there are a few unified approaches to test proof of concept and estimate a target dose, including the multiple comparison procedure using modeling approach, and the permutation approach proposed by Klingenberg. We discuss and compare the operating characteristics of these unified approaches and further develop an alternative approach in a Bayesian framework based on the posterior distribution of a penalized log-likelihood ratio test statistic. Our Bayesian approach is much more flexible to handle linear or nonlinear dose–response relationships and is more efficient than the permutation approach. The operating characteristics of our Bayesian approach are comparable to and sometimes better than both approaches in a wide range of dose–response relationships. It yields credible intervals as well as predictive distribution for the response rate at a specific dose level for the target dose estimation. Our Bayesian approach can be easily extended to continuous, categorical, and time-to-event responses. We illustrate the performance of our proposed method with extensive simulations and Phase II clinical trial data examples.
Clearing of red blood cells in lumbar puncture does not rule out ruptured aneurysm in patients with suspected subarachnoid hemorrhage but negative head CT findings.

BACKGROUND AND PURPOSE In evaluating the results of lumbar puncture (LP), a decrease in the number of red blood cells (RBCs)/mm3 between the first and fourth tubes collected (clearing) has often been assumed to indicate a traumatic puncture rather than the presence of subarachnoid hemorrhage (SAH). We tested the hypothesis that, in the setting of severe headache, CSF clearing coupled with an unremarkable unenhanced CT scan was negatively predictive of the presence of aneurysm and could be used to reduce the need for conventional arteriography. METHODS Cerebral angiography was performed to evaluate suspected SAH in 123 consecutive patients over 2 years at a university teaching hospital. Records of these patients were reviewed. Among the subset without SAH on CT scan, LP results were evaluated for clearing. Clearing was arbitrarily defined as a 25% reduction in RBCs between the first and fourth tubes. This subset's records were also reviewed for the presence of aneurysm at cerebral angiography or at follow-up 6 weeks later. Data were analyzed for correlation between clearing and aneurysm. RESULTS Of the 123 patients whose records were reviewed, 22 did not show an SAH on CT scan. Of those 22 patients, eight had aneurysm at angiography and 14 did not. Clinical diagnoses in the other 14 included trauma, herpes meningitis, sickle cell disease, and cocaine use. CSF clearing was noted in 25% of those with an aneurysm (two of 8) and 21% of those without an aneurysm (three of 14). In the two cases with aneurysms, RBCs cleared from 3550 to 2550 (-28%) and from 24,686 to 17,842 (-28%), respectively. In the remaining six cases with aneurysms, RBCs increased a mean of 1370% between the first and fourth tubes (range, -22% to 7700%). Two of these six had a reduction that did not meet our criteria for clearing (-22% and -5.3%, respectively). In the 14 cases without aneurysms, RBCs increased a mean of 70% between the first and fourth tubes (range, -99% to 895%). In addition to the three of these 14 that met our criteria for clearing (-99%, -99%, and -43%), four cases had a reduction that did not (range, -0.7% to -14%). CONCLUSION A 25% reduction in RBC concentration between the first and fourth tubes of CSF in patients with suspected SAH but negative CT findings occurs even in cases of ruptured aneurysms. Formal evaluation for the presence of an aneurysm is still necessary in this scenario.
Psychological and neural mechanisms of relapse

Relapse, the resumption of drug taking after periods of abstinence, remains the major problem for the treatment of addiction. Even when drugs are unavailable for long periods or when users are successful in curbing their drug use for extended periods, individuals remain vulnerable to events that precipitate relapse. Behavioural studies in humans and laboratory animals show that drug-related stimuli, drugs themselves and stressors are powerful events for the precipitation of relapse. Molecular, neurochemical and anatomical studies have identified lasting neural changes that arise from mere exposure to drugs and other enduring changes that arise from learning about the relationship between drug-related stimuli and drug effects. Chronic drug exposure increases sensitivity of some systems of the brain to the effects of drugs and stressful events. These changes, combined with those underlying conditioning and learning, perpetuate vulnerability to drug-related stimuli. Circuits of the brain involved are those of the mesocorticolimbic dopaminergic system and its glutamatergic connections, and the corticotropin-releasing factor and noradrenergic systems of the limbic brain. This paper reviews advances in our understanding of how these systems mediate the effects of events that precipitate relapse and of how lasting changes in these systems can perpetuate vulnerability to relapse.