Studying Lipophilicity Trends of Phosphorus Compounds by 31P-NMR Spectroscopy: A Powerful Tool for the Design of P-Containing Drugs.

Systematically studying the lipophilicity of phosphorus compounds is of great importance for many chemical and biological fields and particularly for medicinal chemistry. Here, we report on the study of trends in the lipophilicity of a wide set of phosphorus compounds relevant to drug design including phosphates, thiophosphates, phosphonates, thiophosphonates, bis-phosphonates, and phosphine chalcogenides. This was enabled by the development of a straightforward log P determination method for phosphorus compounds based on 31P-NMR spectroscopy. The log P values measured ranged between -3.2 and 3.6, and the trends observed were interpreted using a DFT study of the dipole moments and by H-bond basicity (pKHB) measurements of selected compounds. Clear signal separation in 31P-NMR spectroscopy grants the method high tolerability to impurities. Moreover, the wide range of chemical shifts for the phosphorus nucleus (250 to -250 ppm) enables a direct simultaneous log P determination of phosphorus compound mixtures in a single shake-flask experiment and 31P-NMR analysis.

Nonexponential kinetics captured in sequential unfolding of polyproteins over a range of loads.

While performing under mechanical loads in vivo, polyproteins are vitally involved in cellular mechanisms such as regulation of tissue elasticity and mechano-transduction by unfolding their comprising domains and extending them. It is widely thought that the process of sequential unfolding of polyproteins follows an exponential kinetics as the individual unfolding events exhibit identical and identically distributed (iid) Poisson behavior. However, it was shown that under high loads, the sequential unfolding kinetics displays nonexponential kinetics that alludes to aging by a subdiffusion process. Statistical order analysis of this kinetics indicated that the individual unfolding events are not iid, and cannot be defined as a Poisson (memoryless) process. Based on numerical simulations it was argued that this behavior becomes less pronounced with lowering the load, therefore it is to be expected that polyproteins unfolding under lower forces will follow a Poisson behavior. This expectation serves as the motivation of the current study, in which we investigate the effect of force lowering on the unfolding kinetics of Poly-L8 under varying loads, specifically high (150, 100 â€‹pN) and moderate-low (45, 30, 20 â€‹pN) forces. We found that a hierarchy among the unfolding events still exists even under low loads, again resulting in nonexponential behavior. We observe that analyzing the dwell-time distributions with stretched-exponentials and power laws give rise to different phenomenological trends. Using statistical order analysis, we demonstrated that even under the lowest load, the sequential unfolding cannot be considered as iid, in accord with the power law distribution. Additional free energy analysis revealed the contribution of the unfolded segments elasticity that scales with the force on the overall one-dimensional contour of the energy landscape, but more importantly, it discloses the hierarchy within the activation barriers during sequential unfolding that account for the observed nonexponentiality.

Theoretical investigation of pre-symptomatic SARS-CoV-2 person-to-person transmission in households.

Since its emergence, the phenomenon of SARS-CoV-2 transmission by seemingly healthy individuals has become a major challenge in the effort to achieve control of the pandemic. Identifying the modes of transmission that drive this phenomenon is a perquisite in devising effective control measures, but to date it is still under debate. To address this problem, we have formulated a detailed mathematical model of discrete human actions (such as coughs, sneezes, and touching) and the continuous decay of the virus in the environment. To take into account those discrete and continuous events we have extended the common modelling approach and employed a hybrid stochastic mathematical framework. This allowed us to calculate higher order statistics which are crucial for the reconstruction of the observed distributions. We focused on transmission within a household, the venue with the highest risk of infection and validated the model results against the observed secondary attack rate and the serial interval distribution. Detailed analysis of the model results identified the dominant driver of pre-symptomatic transmission as the contact route via hand-face transfer and showed that wearing masks and avoiding physical contact are an effective prevention strategy. These results provide a sound scientific basis to the present recommendations of the WHO and the CDC.

A single holiday was the turning point of the COVID-19 policy of Israel.

OBJECTIVES: Despite an initial success, Israel's quarantine-isolation COVID-19 policy has abruptly collapsed. This study's aim is to identify the causes that led to this exponential rise in the accumulation of confirmed cases. METHODS: Epidemiological investigation reports were used to reconstruct chains of transmission as well as assess the net contribution of local infections relative to imported cases, infected travelers arriving from abroad. A mathematical model was implemented in order to describe the efficiency of the quarantine-isolation policy and the inflow of imported cases. The model's simulations included two scenarios for the actual time series of the symptomatic cases, providing insights into the conditions that lead to the abrupt change. RESULTS: The abrupt change followed a Jewish holiday, Purim, in which many public gatherings were held. According to the first scenario, the accumulation of confirmed cases before Purim was driven by imported cases resulting in a controlled regime, with an effective reproduction number, Re, of 0.69. In the second scenario, which followed Purim, a continuous rise of the local to imported cases ratio began, which led to an exponential growth regime characterized by an Re of 4.34. It was found that the change of regime cannot be attributed to super-spreader events, as these consisted of approximately 5% of the primary cases, which resulted in 17% of the secondary cases. CONCLUSIONS: A general lesson for health policymakers should be that even a short lapse in public responsiveness can lead to dire consequences.

Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis.

Both monogenic diseases and viral infections can manifest in a broad spectrum of clinical phenotypes that range from asymptomatic to lethal, suggesting that other factors modulate disease severity. Here, we examine the interplay between the genetic neuronopathic Gaucher's disease (nGD), and neuroinvasive Sindbis virus (SVNI) infection. Infection of nGD mice with SVNI had no influence on nGD severity. However, nGD mice were more resistant to SVNI infection. Significantly different inflammatory responses were seen in nGD brains when compared with SVNI brains: the inflammatory response in the nGD brains consisted of reactive astrocytes and microglia with no infiltrating macrophages, but the inflammatory response in the brains of SVNI-infected mice was characterized by infiltration of macrophages and altered activation of microglia and astrocytes. We suggest that the innate immune response activated in nGD confers resistance against viral infection of the CNS.

The Effect of Anesthetic Regimens on Intestinal Absorption of Passively Absorbed Drugs in Rats.

PURPOSE: Different anesthetic regimens are used during single pass intestinal perfusion (SPIP) experiments for the study of intestinal drug absorption in rats. We examined the ketamine/xylazine anesthetic combination to evaluate its influence on drug absorption compared to older regimens. Additionally, we examined whether supplementary analgesia has any effect on drug absorption and the effect of the different anesthetic regimens on induction time and stress response. METHODS: Rats were anesthetized using four different anesthetic regimens; ketamine/midazolam, pentobarbital, ketamine/xylazine and ketamine/xylazine/butorphanol. Three model drugs were administered to rat intestines and Peff was calculated. Stress response was evaluated by quantifying blood corticosterone levels and induction time was recorded. RESULTS: We found absorption under pentobarbital to be higher or similar to absorption under ketamine/midazolam. These results partly correlate with past literature data. Ketamine/xylazine was found to give similar or higher Peff compared to pentobarbital and ketamine/midazolam. Addition of butorphanol did not affect absorption and reduced induction time and stress. CONCLUSIONS: In studies of intestinal drug absorption, the ketamine/xylazine combination is superior to other anesthetic regimens as it is more convenient and seems to affect absorption to a lesser extent. Addition of butorphanol is highly recommended as it did not affect absorption but led to a more effective and less stress inducing experiment.

Correlations within polyprotein forced unfolding dwell-times introduce sequential dependency.

Polyproteins, comprised from proteins arrayed in tandem, respond to mechanical loads through partial unfolding and extension. This response to tension that enables their physiological function is related to the ability to dynamically regulate their elasticity. The unique arrangement of their individual mechanical components (proteins and polymeric linkers), and the interactions between them eventually determines their performance. The sequential unfolding-times within a polyprotein are inherently assumed to be independent and identically distributed (iid), thus expected to follow an exponential distribution. Nevertheless, a large body of literature using single molecule force spectroscopy (SMFS) provides evidence that forced unfolding-times of N proteins within a polyprotein do not follow the exponential distribution. Here we use SMFS with Atomic Force Microscopy to measure the unfolding kinetics of Poly-(I91)8 at 180 pN. The unfolding time-intervals were statistically analysed using three common approaches, all exhibiting an N-effect: hierarchical behavior with non-identical unfolding time distributions. Using continuous time random walk approach indicates that the unfolding times display subdiffusive features. Put together with free-energy reconstruction of the whole unfolding polyprotein, we provide physical explanation for this nontrivial behavior, according to which the elongating polypeptide chain with each unfolding event intervenes with the sequential unfolding probabilities and correlates them.

A new theoretical framework for modeling respiratory protection based on the beta distribution.

The problem of modeling respiratory protection is well known and has been dealt with extensively in the literature. Often the efficiency of respiratory protection is quantified in terms of penetration, defined as the proportion of an ambient contaminant concentration that penetrates the respiratory protection equipment. Typically, the penetration modeling framework in the literature is based on the assumption that penetration measurements follow the lognormal distribution. However, the analysis in this study leads to the conclusion that the lognormal assumption is not always valid, making it less adequate for analyzing respiratory protection measurements. This work presents a formulation of the problem from first principles, leading to a stochastic differential equation whose solution is the probability density function of the beta distribution. The data of respiratory protection experiments were reexamined, and indeed the beta distribution was found to provide the data a better fit than the lognormal. We conclude with a suggestion for a new theoretical framework for modeling respiratory protection.

Frequency Analyses Can Be Improved by a Modified t-test in Sample-based Preclinical Efficacy Studies.

Sample-based preclinical drug efficacy studies compare frequency (proportion) or incidences of successes within respective samples of test and control groups. The word success in principle refers to a protected (e.g., due to vaccination), recovered, or surviving animal, depending on the particular experiment. We introduce here a modified t-test for two independent groups, aimed at statistical analysis of the difference between frequencies of successes in sample based preclinical studies. The test is applicable whenever the study is based on repeating replicate experiments, as required by certain procedures such as validation. Such experiments are based on constant drug dose and performed under identical conditions and protocol. The proposed test combines the computational rules of t-test for two independent groups and analysis of variance. In the initial steps, incidences are transformed to proportions, and variance between proportions in samples of the j(th) group (s(p(j))(2)), is then transformed into theoretical weighted variance within the i(th) repetition (sample) of the j(th) group (s(i,j)(2)). The variance of proportions in samples of the size of the whole group (SE(j)(2)) is then calculated. The t-statistic is computed according to the rules of t-test for two independent groups. Significance is calculated using (N(1) - 1) + (N(2) - 1) degrees of freedom, where N(j) denotes the total number of animals in the j(th) group. The proposed model offers an important advantage over incidence or proportion distribution models, such as chi-square or normal approximation of binomial distribution, respectively, because it considers variance between replicate experiments. It moreover offers important flexibility by limiting the requirement for identical sample sizes only to samples within the control or test group. A difference between groups in sample sizes, number of samples, or both, preventing application of block designs or the standard formats of t-test, may still exist. Theoretical considerations and working examples are provided. LAY ABSTRACT: Sample based preclinical drug efficacy studies compare frequency (proportion) or incidences of successful results (e.g., protected, recovered, or surviving animals, depending on the particular experiment) within respective samples of the test and the control groups. Certain procedures, such as validation, require replicate experiments that are identical in all controllable factors, such as drug dose, sample sizes within each group, general experimental conditions, etc. Still, the control sample size is not required to be identical to that of the respective test sample size. In such cases, t-test or block designs are not applicable for statistical analyses. Moreover, incidence or frequency distribution models, such as chi-square or normal approximation of binomial distribution, respectively, which are performed on pooled data of the examined groups, ignore variance between experiments and thereby result in impaired validity of the statistical inference. We propose here a modified t-test that limits the requirement for identical sample sizes to only within each group. This aim is achieved by combining the computational rules of t-test together with analysis of variance. The proposed t-test allows the incorporating of variance between experiments into frequency or incidence assessments. We recommend using the proposed modified t-test as a complementary test to incidence distribution models.

Circulation of bovine ephemeral fever in the Middle East--strong evidence for transmission by winds and animal transport.

Bovine ephemeral fever virus (BEFV) is an economically important arbovirus of cattle. The main routes of its transmission between countries and continents are not completely elucidated. This study aimed to explore BEFV transmission in the Middle-East. A phylogenetic analysis was performed on the gene encoding the G protein of BEFV isolates from Israel from 2000 and 2008 with isolates from Turkey (2008), Egypt (2005), Australia (1968-1998) and East Asia (1966-2004). Calf sera collected during the years 2006-2007 were tested by serum neutralization in order to explore for recent exposure to BEFV before 2008. These were followed by a meteorological analysis, aimed to reveal movement of air parcels into Israel in the two weeks preceding the first case of BEF in Israel in 2008. The 2008 Israeli and Turkish isolates showed 99% identity and formed a new cluster with the 2000 Israeli isolate. The serological survey showed no new exposure to BEFV during 2006 and 2007. These results coincided with the meteorological analysis, which revealed that air parcels originating in Southern Turkey had reached the location of outbreak onset in Israel nine days before the discovery of the index case. The Egyptian isolate clustered phylogenetically with the Taiwanese isolates, coinciding with data on importation of cattle from China to the Middle East in the year preceding the isolation of the Egyptian isolates. These results suggest that both winds and animal transport may have an important role in trans-boundary transmission of BEFV.