Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of a Mycobacterium smegmatis gene that confers resistance to phages L5 and D29 when overexpressed

Bacteriophage infection requires a specific interaction with the outer surface of a bacterial host followed by interaction with the cell membrane and phage DNA injection. Phages of the mycobacteria encounter a cell wall that is rich in unusual lipid‐ and sugar‐containing components which form a formidable barrier that must be passed to gain access to the membrane. We describe here a gene of Mycobacterium smegmatis that confers resistance to mycobacteriophages L5 and D29. The phage‐resistance phenotype results not from mutation but from elevated expression of a wild‐type gene. It appears that the product of this multicopy phage‐resistance (mpr) gene may alter the structure of the host cell wall or membrane, thereby inhibiting productive phage DNA injection.
Minimal requirements for the cultural evolution of language

Human language is both a cognitive and a cultural phenomenon. Any evolutionary account of language, then, must address both biological and cultural evolution. In this thesis, I give a mainly cultural evolutionary answer to two main questions: firstly, how do working systems of learned communication arise in populations in the absence of external or internal guidance? Secondly, how do those communication systems take on the fundamental structural properties found in human languages, i.e. systematicity at both a meaningless and meaningful level? A large, multi-disciplinary literature exists for each question, full of apparently conflicting results and analyses. My aim in this thesis is to survey this work, so as to find any commonalities and bring this together in order to provide a minimal account of the cultural evolution of language. The first chapter of this thesis takes a number of well-established models of the emergence of signalling systems. These are taken from several different fields: evolutionary linguistics, evolutionary game theory, philosophy, artificial life, and cognitive science. By using a common framework to directly compare these models, I show that three underlying commonalities determine the ability of any population of agents to reliably develop optimal signalling. The three requirements are that i) agents can create and transfer referential information, ii) there is a systemic bias against ambiguity, and iii) some mechanism leading to information loss exists. Following this, I extend the model to determine the effects of including referential uncertainty. I show that, for the group of models to which this applies, this places certain extra restrictions on the three requirements stated above. In the next chapter, I use an information-theoretic framework to construct a novel analysis of signalling games in general, and rephrase the three requirements in more formal terms. I then show that we can use these 3 criteria as a diagnostic
Estimating Private Sector Professional Fees for VA Providers

Objectives. To describe new methods used to estimate inpatient and outpatient Medicare-based professional fees for Veterans Health Administration (VA) services. Methods. National VA utilization files provided estimates of inpatient physician services, whereas local provider and utilization files gave counts of outpatient services by physicians, nurse practitioners, physician assistant, clinical psychologists, and clinical social workers. Services from ambulatory surgery, emergency room, and clinics (eg, dermatology and gastroenterology) were coded by study health information management staff (coders). VA-based billing information was edited against Medicare guidelines. Estimates for VA services without comparable Medicare fees were obtained from other commercial sources. ResultsHypothetical professional fees for VA services were 17% more ($109 million vs. $93 million) than the VA budget for physicians over 1 fiscal year at six sites. Total payments of nearly $21 million were generated for VA inpatient care. In fiscal year 1999, there were 30,209 admissions (of which 4549 were psychiatric) to the study sites; 30,518 discharges; 229,783 inpatient days, including 27,235 in critical care units; and 38,348 surgical days of care. Discussion. Differences between the VA and the private sector maybe overstated because VA salaries of nonphysicians were not included in the VA budgets. Conversely, the extent to which VA professional services were undercounted in VA information systems used in this study may understate the difference. Future research may consider additional data collection approaches or information systems enhancements to enumerate more accurately all provider services that are reimbursable in the private sector.
Outcomes of Trauma-Informed Interventions for Incarcerated Women

The purpose of this article was to conduct a review of experimental, quasi-experimental, and pre-test/post-test studies using manualized, trauma-informed interventions with incarcerated women. A systematic search of electronic databases, reference harvesting, and communication with experts were used to identify relevant primary studies. Nine studies meeting the specified inclusion/exclusion criteria were identified. Three studies used random assignment and five used a comparison or waitlist group. Interventions identified included Seeking Safety, Helping Women Recover/Beyond Trauma, Esuba, and Beyond Violence. Results of the studies indicate a decrease in post-traumatic stress disorder (PTSD) symptomatology and an additive effect to treatment as usual. Initial evidence for trauma-informed interventions for incarcerated women appears positive; however, replication using more rigorous research designs and inclusion of effect sizes are recommended. Limitations of this review include exclusion of the gray literature and lack of meta-analysis.
A Hybrid method for effective multiple sequence alignment

Progressive methods for multiple sequence alignment are popular for their simplicity and cost effectiveness. However, it has been shown that they fail in locating the flanking core blocks. To cope with this issue, we describe in this paper a hybrid algorithm that aims to improve the accuracy of progressive global alignments especially in the case of families including sequences with large NC-terminal extension. The key idea is to combine local and global alignments within the same alignment process. This process acts as a progressive method driven by a guide tree where pairwise local or global alignment is performed depending on the significance of the difference between lengths of sequences. Experiments on a wide range of data sets have shown the effectiveness of the proposed framework and its ability to achieve good quality solutions.
Dealing with the curse of dimensionality in systems and control: The randomization paradigm

Randomized algorithms have gained increasing popularity in the systems and control community for their ability of dealing in an efficient way with complex systems affected by uncertainty. In particular, at the expense of accepting a predetermined risk of failure, they allow to cope with the complexity/conservatism barriers of classical robust control and optimization methods. In this tutorial paper, we first briefly overview the main results for addressing probabilistic robust optimization problems using a randomized approach, in particular focusing on recent results that allow iterative and distributed implementations. Then, we show how the use of randomization proved to be a key tool in the development of distributed schemes for the solution of problems involving large amounts of data, as the well-known Google PageRank problem. Finally, we overview theoretical computer science and numerical linear algebra approaches for the solution of least-squares problems and low-rank matrix approximations, for the case when the matrices involved are of very large scale. These results, which go under the name of randomized matrix algorithms, may prove very useful in the context of systems estimation and control.
Evolutionary Game Analysis of Financial Regulation and Innovation Under Asymmetric Conditions

The loose financial supervision and excessive financial innovation will lead the country to heavy losses in financial crisis. So how to balance the relationship between financial supervision and financial innovation and make financial supervision and financial innovation to achieve complementary has become a hot issue. The financial supervision and financial institutions are a process of repeated game, but the research on them is still in a superficial stage. Therefore, this paper uses evolutionary game theory and method to analyze the dynamic replication system of asymmetric evolutionary game of two groups of financial institutions and regulators in China. And the evolutionary stable state of the system under different conditions is analyzed. The conclusion is that under different parameter values, the other side adopts different strategies, and the system will tend to different equilibrium states.
The influence of power relations on English L1 and L2 speakers' oral requests

Recently, there has been a broader emphasis on studying the influence of social factors on phonetic realizations. Given that the second language learners’ performances of speech acts differ significantly from the native speakers, investigating and acknowledging the social differences which affect the prosodic variations is the first step to make learners aware of the appropriate use of the speech acts in the target language. The current paper examines the differences in English L1 and L2 speakers’ “request. ” The participants for this study were 16 Korean EFL speakers and 9 English native speakers. Twelve English request sentences were elicited by the participants as responses to situation prompts (4 tokens for three power relations: power high, equal, and low). The speech variations (e.g., pitch, intensity, and speech rate) were analyzed with Praat. The findings indicated that L2, but not L1, speakers tended to slow down their pace in a power-high situation. Pitch results revealed that Korean male speakers lowered their pitch to mitigate difficult requesting situations. Moreover, the verbal report showed that all except one Korean EFL speakers felt that requesting to professors was the hardest whereas all but one English natives responded that requesting to strangers was the most difficult.
Atomic force microscopy to characterize the molecular size of prion protein

The conformational transition of α‐helix‐rich cellular prion protein (PrPC) to an isomer with high β‐sheet content is associated with transmissible spongiform encephalopathies. With the ultimate long‐term goal of using imaging techniques to study PrP aggregation, we report the results of initial experiments to determine whether PrP molecules could be visualized as single molecules, and if the observed size corresponded to the calculated size for PrP. The investigation of single molecules, and not those embedded into larger aggregates, was the key in our experimental approach. Using atomic force microscopy (AFM) as an imaging method, the immobilization of recombinant histidine (His)10‐tagged PrP on mica was performed in the presence of different heavy metal ions. The addition of Cu2+ resulted in an enhanced PrP immobilization, whereas Ni2+ reduced coverage of the surface by PrP. High‐resolution data from dried PrP preparations provided a first approximation to geometrical parameters of PrP precipitates, which indicated that the volume of a single PrP molecule was 30 nm3. Molecular dynamics simulations performed to complement the structural aspects of the AFM investigation yielded a calculated molecular volume of 33 nm3 for PrP. These experimentally observed and theoretically expected values provide basic knowledge for further studies on the size and composition of larger amyloidal PrP aggregates, PrP isoforms or mutants such as PrP molecules without octarepeats.
Location and Extent of Deep Vein Thrombosis in Patients with and without FV:R 506Q Mutation

Summary Resistance to activated protein C due to FV:R 506Q mutation is the most common known genetic risk factor for deep leg vein thrombosis (DVT). The aim of this prospective study was to describe and compare the location and extent of DVT, reflected by a scoring system, in a group of patients with and without FV:R 506Q mutation. Of 247 consecutively included patients undergoing phlebography 105 had a DVT, 36 (35%) in the FV:R 506Q mutation group and 69 (65%) in the non-FV:R 506Q mutation group. Compared to the non-FV:R 506Q mutation group there was a significant increase in the incidence of DVT in the FV:R 506Q mutation group (p = 0.041, OR = 1.79 [1.02–3.15]), a significantly lower mean DVT score of the iliofemoral vein segments (p = 0.0081) and a significantly lower incidence of DVT in the iliofemoral vein segments (p = 0.007, OR = 10.6 [1.3–83.3]), 1/36 (2.8%) compared to 16/69 (23.2%). As controls 288 blood donors were included, with and without FV:R 506Q mutation and with no history of DVT in order to evaluate risk factors of DVT. The odds ratio of an iliofemoral DVT was 0.5 ([0.06–3.90), p = 0.50]) when FV:R 506Q mutation was present, compared to the control group, and at locations below the iliofemoral segments 5.28 ([3.01–9.28], p = less than 0.0001). Our findings provide the basis of a detailed phlebographic description and for the first time, to our best knowledge, shows a specific phlebographic pattern that may be linked to an inherited hypercoagulable state.
A plasma membrane‐associated AAA‐ATPase from Glycine max

An AAA‐ATPase (ATPases Associated with a Variety of Cellular Activities) localized to the plasma membrane of soybean (Glycine max) was isolated, partially sequenced and cloned (SBPM AAA‐ATPase). The protein with an apparent monomer molecular mass of about 97 kDa was isolated using a combination of anion exchange, preparative SDS‐PAGE, reverse phase HPLC, and ATP affinity chromatography. The cDNA for the full‐length SBPM AAA‐ATPase was cloned by screening an expression library using an antibody against the highly conserved Walker B AAA‐ATP‐binding motif. Northern blot analysis detected one transcript of ∼2700 bp. The full‐length cDNA sequence was that previously obtained (GenBank Database; U20213) encoding a protein with two copies of the conserved AAA‐ATP‐binding motif and regions of sequence homology with other AAA‐ATPases. Electron microscopic preparations of the recombinant SBPM AAA‐ATPase revealed hexamers typically formed by these proteins. The cloned and expressed protein was identical to the protein isolated from the soybean plasma membrane as confirmed using antisera raised to a non‐conserved region of the derived protein sequence and by N‐terminal sequencing of peptides derived from the isolated protein.
Output cluster synchronization of heterogeneous linear multi-agent systems

This paper considers the cluster synchronization problem for coupled agents which are described by heterogeneous linear dynamic models. The aim is to synchronize the outputs of the agent systems belonging to the same cluster. This problem is solved by incorporating a common internal reference system into agent systems belonging to the same cluster while in different clusters the internal reference systems are assumed to have nonidentical linear dynamics. This paper proposes a leaderless control law for each agent, and derives a necessary and sufficient algebraic condition which relates parameters from the interaction graph and the internal models. This condition is shown to be satisfied if the interaction graph admits a directed spanning tree in each cluster and the coupling strengths among agents are strong enough.
Population modeling for a captive squirrel monkey colony

Population modeling for a squirrel monkey colony breeding in a captive laboratory environment was approached with the use of two different mathematical modeling techniques. Deterministic modeling was used initially on a spreadsheet to estimate future census figures for animals in various age/sex classes. Historical data were taken as input parameters for the model, combined with harvesting policies to calculate future population figures in the colony. This was followed by a more sophisticated stochastic model that is capable of accommodating random variations in biological phenomena, as well as smoothing out measurement errors. Point estimates (means) for input parameters used in the deterministic model are replaced by probability distributions fitted into historical data from colony records. With the use of Crystal Ball® (Decisioneering, Inc., Denver, CO) software, user‐selected distributions are embedded in appropriate cells in the spreadsheet model. A Monte Carlo simulation scheme running within the spreadsheet draws (on each cycle) random values for input parameters from the distribution embedded in each relevant cell, and thus generates output values for forecast variables. After several thousand runs, a distribution is formed at the output end representing estimates for population figures (forecast variables) in the form of probability distributions. Such distributions provide the decision‐maker with a mathematical habitat for statistical analysis in a stochastic setting. In addition to providing standard statistical measures (e.g., mean, variance, and range) that describe the location and shape of the distribution, this approach offers the potential for investigating crucial issues such as conditions surrounding the plausibility of extinction. Am. J. Primatol. 65:239–254, 2005. © 2005 Wiley‐Liss, Inc.
Effect of Hypocapnia on Extracellular Glutamate and Glycine Concentrations during the Periischemic Period in Rabbit Hippocampus a

Glutamate (GLU) is a neurotransmitter. Massive release of GLU and glycine (GLY) into the brain's extracellular space may be triggered by ischemia, and may result in acute neuronal lysis or delayed neuronal death. The aim of this study was to evaluate the possible relationship between hyperventilation and the level of GLU and GLY during brain ischemia. Rabbits were anesthetized with halothane and oxygen. Group 1 was allowed to hyperventilate (PaCO2 25-35 mmHg). PaCO2 was maintained throughout the study. Group 2 was a normal control group that maintained normocapnia. Two global cerebral ischemic episodes were produced. Microdialysate was collected during the periischemic and reperfusion periods from the dorsal hippocampus. GLU and GLY concentrations were determined using high-performance liquid chromatography. In the control group, GLU and GLY were significantly elevated during each episode of ischemia; these levels returned to baseline within 10 minutes after reperfusion. In contrast, in the hyperventilation group GLU and GLY concentrations increased during ischemia, but they were not statistically significant. Two way ANOVA for the periischemic periods (t = 15,80; p = 0.06) revealed lower GLU values for the hyperventilated animals. A similar analysis for periischemic GLY concentrations revealed significantly lower values in the hyperventilated group (t = 10,15,75,80: p = 0.03) as compared to normal controls. We were able to demonstrate that hypocapnia during periischemic period lowered extracellular GLU and GLY concentrations. These results can explain a part of the protective action of hypocapnia during cerebral ischemia.
Interleukin 10 (IL-10)-mediated Immunosuppression

Background: IL-10 suppresses antigen presentation by macrophages (MΦ) and dendritic cells (DCs). Results: IL-10 promotes expression of the MHC class II and CD86 E3 ubiquitin ligase March-I and suppresses antigen presentation in activated MΦ but not in DCs. Conclusion: IL-10 suppression of antigen presentation is March-I-dependent in MΦ but March-I-independent in DCs. Significance: IL-10 suppresses antigen presentation in MΦ and DCs by distinct molecular mechanisms. Efficient immune responses require regulated antigen presentation to CD4 T cells. IL-10 inhibits the ability of dendritic cells (DCs) and macrophages to stimulate antigen-specific CD4 T cells; however, the mechanisms by which IL-10 suppresses antigen presentation remain poorly understood. We now report that IL-10 stimulates expression of the E3 ubiquitin ligase March-I in activated macrophages, thereby down-regulating MHC-II, CD86, and antigen presentation to CD4 T cells. By contrast, IL-10 does not stimulate March-I expression in DCs, does not suppress MHC-II or CD86 expression on either resting or activated DCs, and does not affect antigen presentation by activated DCs. IL-10 does, however, inhibit the process of DC activation itself, thereby reducing the efficiency of antigen presentation in a March-I-independent manner. Thus, IL-10 suppression of antigen presenting cell function in macrophages is March-I-dependent, whereas in DCs, suppression is March- I-independent.
Abnormal P600 word repetition effect in elderly persons with preclinical Alzheimer’s disease

We sought cognitive event-related potential (ERP) biomarkers of “Preclinical Alzheimer’s disease” (Pre-AD) using an incidental verbal learning paradigm with high sensitivity to prodromal AD. Seven elderly persons, with normal cognition at the time of ERP recordings, but who showed subsequent cognitive decline or AD pathology at autopsy (n = 5, mean Braak stage = 2.8), were compared to 12 “robust” normal elderly (RNE) persons who remained cognitively normal (Mfollow-up = 9.0 years). EEG was recorded during a word repetition paradigm (semantically congruous (50%) and incongruous target words repeat ~10–140 seconds later). The RNE P600 congruous word repetition ERP effects (New minus Old congruous words) were significantly larger than in Pre-AD (mean amplitudes = 3.28 vs. 0.10 μV, p = .04). High group discrimination (84%) was achieved (by a P600 amplitude cutoff of ~1.5 μV). Abnormal P600 word repetition effects in cognitively normal elderly persons may be an important sign of synaptic dysfunction and Preclinical AD.
Dinitrogen Production from Nitrite by a Nitrosomonas Isolate

A chemolithotrophic ammonium-oxidizing bacterium that was able to reduce 15NO2− to 15N2 (m/z 30) while oxidizing ammonium under conditions of oxygen stress was isolated from stream sediments. Energy was derived from ammonium oxidation, as evidence by growth, with CO2 serving as the sole C source. The organism was a gram-negative, motile, short rod that failed to grow either aerobically or anaerobically in heterotroph media. The organism was identified as a Nitrosomonas sp.
Lethal mutagenesis, error thresholds, and the fight against viruses: Rigorous modeling is facilitated by a firm physical background

V iroids and viruses can be viewed as ultimate parasites, which exploit the host through entering cells and manipulating cellular metabolism for their own reproduction. Proliferation of viruses is bound to successful replication of virus genomes, RNA or DNA, where successful implies viable virus progeny, that is, capable of reproduction. Viroids are naked RNA molecules and therefore entirely dependent on host biochemistry. The genomic RNA of simple bacteriophages mimics messenger RNAs of the host cell and it is recognized and translated by host ribosomes. Simple virus genomes encode for a few proteins only, commonly for (i) a virus specific RNA replicase or at least a subunit of a replicase, which takes care that virus RNA and not cellular RNA is replicated preferentially, (ii) a protein for coating the virus RNA, and (iii) a protein that initiates lyses of the cell. As Charles Weissmann [1] pointed out already in the 1970s, in simple cases the life cycles of phages in bacterial cells are encoded by the structure of the genomic virus RNA and her unfolding–folding dynamics. Forty years ago Manfred Eigen [2] published a kinetic theory of evolution at the molecular level, that is, directly applicable to replication of viral RNA. Among other things, one major characteristic of this theory is the handling of mutations: Correct replication and mutations are treated as parallel chemical reactions and this has the advantage that the approach applies equally well to the whole range of mutation rates from very small to large. The kinetic mutation selection equations of the model proposed by Eigen for N different variants Xj in the population are: