Miracle-dz/UniFAR-FTUs huggingface dataset:
A new adaptive local linear prediction method and its application in hydrological time series.

The embedding dimension and the number of nearest neighbors are very important parameters in the prediction of a chaotic time series. In order to reduce the uncertainties in the determination of the forgoing two parameters, a new adaptive local linear prediction method is proposed in this study. In the new method, the embedding dimension and the number of nearest neighbors are combined as a parameter set and change adaptively in the process of prediction. The generalized degree of freedom is used to help select the optimal parameters. Real hydrological time series are taken to examine the performance of the new method. The prediction results indicate that the new method can choose the optimal parameters of embedding dimension and the nearest neighbor number adaptively in the prediction process. And the nonlinear hydrological time series perhaps could be modeled better by the new method.
Human Gut-Commensalic Lactobacillus ruminis ATCC 25644 Displays Sortase-Assembled Surface Piliation: Phenotypic Characterization of Its Fimbrial Operon through In Silico Predictive Analysis and Recombinant Expression in Lactococcus lactis

Sortase-dependent surface pili (or fimbriae) in Gram-positive bacteria are well documented as a key virulence factor for certain harmful opportunistic pathogens. However, it is only recently known that these multi-subunit protein appendages are also belonging to the “friendly” commensals and now, with this new perspective, they have come to be categorized as a niche-adaptation factor as well. In this regard, it was shown earlier that sortase-assembled piliation is a native fixture of two human intestinal commensalics (i.e., Lactobacillus rhamnosus and Bifidobacterium bifidum), and correspondingly where the pili involved have a significant role in cellular adhesion and immunomodulation processes. We now reveal that intestinal indigenous (or autochthonous) Lactobacillus ruminis is another surface-piliated commensal lactobacillar species. Heeding to in silico expectations, the predicted loci for the LrpCBA-called pili are organized tandemly in the L. ruminis genome as a canonical fimbrial operon, which then encodes for three pilin-proteins and a single C-type sortase enzyme. Through electron microscopic means, we showed that these pilus formations are a surface assemblage of tip, basal, and backbone pilin subunits (respectively named LrpC, LrpB, and LrpA) in L. ruminis, and also when expressed recombinantly in Lactococcus lactis. As well, by using the recombinant-piliated lactococci, we could define certain ecologically relevant phenotypic traits, such as the ability to adhere to extracellular matrix proteins and gut epithelial cells, but also to effectuate an induced dampening on Toll-like receptor 2 signaling and interleukin-8 responsiveness in immune-related cells. Within the context of the intestinal microcosm, by wielding such niche-advantageous cell-surface properties the LrpCBA pilus would undoubtedly have a requisite functional role in the colonization dynamics of L. ruminis indigeneity. Our study provides only the second description of a native-piliated Lactobacillus species, but at the same time also involves the structural and functional characterization of a third type of lactobacillar pilus.
Ultra scale‐down of protein refold screening in microwells: Challenges, solutions and application

Steps for the refolding of proteins from solubilized inclusion bodies or misfolded product often represent bottlenecks in process development, where optimal conditions are typically derived empirically. To expedite refolding optimization, microwell screening may be used to test multiple conditions in parallel. Fast, accurate, and reproducible assays are required for such screening processes, and the results derived must be representative of the process at full scale. This article demonstrates the use of these microscale techniques to evaluate the effects of a number of additives on the refolding of IGF‐1 from denatured inclusion bodies, using an established HPLC assay for this protein. Prior to this, microwell refolding was calibrated for scale‐up using hen egg‐white lysozyme (HEWL) as an initial model protein, allowing us to implement and compare several assays for protein refolding, including turbidity, enzyme activity, and chromatographic methods, and assess their use for microwell‐based experimentation. The impact of various microplate types upon protein binding and loss is also assessed. Solution mixing is a key factor in protein refolding, therefore we have characterized the effects of different methods of mixing in microwells in terms of their impact on protein refolding. Our results confirm the applicability and scalability of microwell screening for the development of protein refolding processes, and its potential for application to new inclusion body‐derived protein products. Biotechnol. Bioeng. 2009;103: 329–340. © 2008 Wiley Periodicals, Inc.
What Do Boards Really Do? Evidence from Minutes of Board Meetings

Abstract We analyze a unique database from a sample of real-world boardrooms — minutes of board meetings and board-committee meetings of eleven business companies for which the Israeli government holds a substantial equity interest. We use these data to evaluate the underlying assumptions and predictions of models of boards of directors. These models generally fall into two categories: “managerial models” that assume boards play a direct role in managing the firm, and “supervisory models” that assume that boards monitor top management but do not make business decisions themselves. Consistent with the supervisory models, our minutes-based data suggest that boards spend most of their time monitoring management: approximately two-thirds of the issues boards discussed were of a supervisory nature, they were presented with only a single option in 99% of the issues discussed, and they disagreed with the CEO only 2.5% of the time. Nevertheless, at times boards do play a managerial role: Boards requested to receive further information or an update for 8% of the issues discussed, and they took an initiative with respect to 8.1% of them. In 63% of the meetings, boards took at least one of these actions or did not vote in line with the CEO. Taken together our results suggest that boards can be characterized as active monitors.
Error analysis for encoding a qubit in an oscillator (5 pages)

In Phys. Rev. A 64, 012310 (2001), Gottesman, Kitaev, and Preskill described a method to encode a qubit in the continuous Hilbert space of an oscillator's position and momentum variables. This encoding provides a natural error-correction scheme that can correct errors due to small shifts of the position or momentum wave functions (i.e., use of the displacement operator). We present bounds on the size of correctable shift errors when both qubit and ancilla states may contain errors. We then use these bounds to constrain the quality of input qubit and ancilla states.
Genomic sweep and potential genetic rescue during limiting environmental conditions in an isolated wolf population

Genetic rescue, in which the introduction of one or more unrelated individuals into an inbred population results in the reduction of detrimental genetic effects and an increase in one or more vital rates, is a potentially important management tool for mitigating adverse effects of inbreeding. We used molecular techniques to document the consequences of a male wolf (Canis lupus) that immigrated, on its own, across Lake Superior ice to the small, inbred wolf population in Isle Royale National Park. The immigrant's fitness so exceeded that of native wolves that within 2.5 generations, he was related to every individual in the population and his ancestry constituted 56 per cent of the population, resulting in a selective sweep of the total genome. In other words, all the male ancestry (50% of the total ancestry) descended from this immigrant, plus 6 per cent owing to the success of some of his inbred offspring. The immigration event occurred in an environment where space was limiting (i.e. packs occupied all available territories) and during a time when environmental conditions had deteriorated (i.e. wolves' prey declined). These conditions probably explain why the immigration event did not obviously improve the population's demography (e.g. increased population numbers or growth rate). Our results show that the beneficial effects of gene flow may be substantial and quickly manifest, short-lived under some circumstances, and how the demographic benefits of genetic rescue might be masked by environmental conditions.
Semianalytical Estimation of Energy Deposition in the Ionosphere by Monochromatic Alfvén Waves

For the first time we derive an analytical expression for energy deposition by propagating monochromatic Alfvén waves in the collisional ionosphere‐thermosphere (IT). Based on empirical models of IT parameters, we show an approximately 10% increase in efficiency of energy deposition at high latitudes and about 150 km altitude by Alfvén waves at 5 Hz as compared to static fields of the same magnitude. We analyze the dependence of the wave energy deposition on geomagnetic activity through a Global Ionosphere‐Thermosphere Model (GITM) simulation of IT conditions during the 13–14 October 2016 geomagnetic storm. The peak Alfvén wave contribution occurs in the E layer and lower part of the F layer. Wave‐induced heating is shown to increase in the daytime and postdusk high‐latitude F layer during the storm due to increased wave‐modified conductivity. We estimate that the Alfvén wave contribution to the IT energy budget can reach about 30% of the value of static Joule heating during a strong storm and that the actual percentage increase is dependent on latitude and altitude. This effect carries important implications for ionospheric dynamics, especially for density enhancement in the daytime cusp, heating in the vicinity of auroral arcs and ion outflow.
Influenza vaccine effectiveness in preventing hospitalization among the elderly during influenza type A and type B seasons.

BACKGROUND Influenza vaccine effectiveness evaluations were carried out among the elderly, as part of a demonstration established to estimate the value of including influenza vaccination as a covered Medicare benefit. METHODS Cases hospitalized with pneumonia and influenza-related diagnoses during November through April were identified and group matched to randomly selected community controls. Data were collected from cases and controls on influenza vaccination status and other factors which could have confounded the association between vaccination and hospitalization. A community-based influenza surveillance programme was conducted each year to determine the timing and aetiology of influenza activity. Logistic regression analyses were carried out to evaluate the association of influenza vaccination with the likelihood of hospitalization. RESULTS In 1990-1991, during the peak of the influenza type B outbreak, influenza vaccination was estimated to be 31% (95% CI: 4-51%) effective in reducing the likelihood of hospitalization. In 1991-1992, during the peak of the influenza type A(H3N2) epidemic, a nearly identical point estimate for vaccine effectiveness was demonstrated (32%, 95% CI: 7-50%). Identical analyses carried out each year during the periods of low or absent influenza activity failed to demonstrate a significant effect for vaccination in preventing hospitalization. CONCLUSION Results indicated that a significant benefit for vaccination could be expected during both type A and type B influenza seasons.
Risk factors for violent death of women in the home.

OBJECTIVES To determine risk factors for violent death of women in the home, and particularly, to assess the strength and direction of any association between domestic violence or keeping firearms and homicide or suicide in the home. METHODS Subgroup analysis of a large population-based case-control study database was performed, defining cases as all homicides and suicides occurring in the homes of female victims in 3 metropolitan counties: Shelby County, Tennessee; King County, Washington; and Cuyahoga County, Ohio. Randomly selected control subjects were matched to the victims by neighborhood, sex, race, and age range. Exposures to potential risk factors were ascertained by interviewing a proxy for the victim 3 to 6 weeks after the violent death occurred. These answers were compared with those obtained from controls using matched-pairs methods. RESULTS All cases (n = 266) were identified in the 3-county area, including 143 homicides and 123 suicides, during a 5-year period. Matching controls (n = 266) were also identified. Firearms were involved in 46% of the homicides and 42% of the suicides. Independent risk factors for suicide in the home included a history of mental illness (odds ratio [OR], 258.8; 95% confidence interval [CI], 18.2-3679.8), living alone (OR, 13.4; 95% CI, 2.0-87.8), and having 1 or more guns in the home (OR, 4.6; 95% CI, 1.2-17.5). Independent risk factors for homicide included living alone (OR, 5.1; 95% CI, 2.0-13.2), illicit drug use by any member of the household (OR, 4.9; 95% CI, 1.3-15.9), prior domestic violence (OR, 4.0; 95% CI, 1.5-10.5), 1 or more guns in the home (OR, 3.4; 95% CI, 1.6-7.1), and previous arrest of any member of the household (OR, 3.0; 95% CI, 1.3-6.6). The increased risk of homicide associated with domestic violence, firearms, or illicit drugs was attributable to the homicides at the hands of a spouse, intimate acquaintance, or close relative. CONCLUSIONS Among women, mental illness and living alone increase the risk of suicide in the home, and household use of illicit drugs and prior domestic violence increase the risk of homicide. Instead of conferring protection, keeping a gun in the home is associated with increased risk of both suicide and homicide of women. Household use of illicit drugs, domestic violence, and readily available firearms place women at particularly high risk of homicide at the hands of a spouse, an intimate acquaintance, or a close relative. Many factors place women at increased risk of violent death in the home. Community- and clinic-based interventions should target those with identifiable risk factors.
CORE Scholar CORE Scholar

We introduce description logic (DL) rules as a new rule-based formalism for knowledge representation in DLs. As a fragment of the Semantic Web Rule Language SWRL, DL rules allow for a tight integration with DL knowledge bases. In contrast to SWRL, however, the combination of DL rules with expressive description logics remains decidable, and we show that the DL SROIQ – the basis for the ongoing standardisation of OWL 2 – can completely internalise DL rules. On the other hand, DL rules capture many expressive features of SROIQ that are not available in simpler DLs yet. While reasoning in SROIQ is highly intractable, it turns out that DL rules can be introduced to various lightweight DLs without increasing their worst-case complexity. In particular, DL rules enable us to signiﬁcantly extend the tractable DLs EL ++ and DLP.
The Effect of a Pilot Pediatric In-Patient Department-Based Smoking Cessation Intervention on Parental Smoking and Children’s Secondhand Smoke (SHS) Exposure in Guangxi, China

Children’s exposure to secondhand smoke (SHS) at home has numerous adverse health effects. This study evaluated the effects of a pediatric in-patient department-based pilot smoking cessation intervention for household members to reduce children’s SHS exposure and encourage smoking cessation. A pre-post test design study was designed to assess the effectiveness of a telephone counseling intervention on household members of hospitalized children in pediatric departments. Data were collected with a standardized Chinese language questionnaire. At the three-month follow-up survey, the proportions of household members who reported adopting complete smoking restriction at home (55%), did not smoke at home at all (37%), did not allow others to smoke in the car (70%), or did not allow others to smoke around the child (57%) were significantly higher than the self-reported responses at the baseline survey. The proportions of household members who reported smoking at home (49%) and in the car (22%) were significantly lower than the baseline survey. Overall, 7% of the participants had reported quitting smoking after three months. Pediatric in-patient department-based telephone counseling for smoking cessation was found to be acceptable to Chinese parents. The intervention encouraged few parents to quit smoking, but encouraged more parents to take measures to reduce children’s SHS exposure.
CompactDFA: Scalable Pattern Matching Using Longest Prefix Match Solutions

A central component in all contemporary intrusion detection systems (IDSs) is their pattern matching algorithms, which are often based on constructing and traversing a deterministic finite automaton (DFA) that represents the patterns. While this approach ensures deterministic time guarantees, modern IDSs need to deal with hundreds of patterns, thus requiring to store very large DFAs, which usually do not fit in fast memory. This results in a major bottleneck on the throughput of the IDS, as well as its power consumption and cost. We propose a novel method to compress DFAs by observing that the name used by common DFA encoding is meaningless. While regular DFAs store separately each transition between two states, we use this degree of freedom and encode states in such a way that all transitions to a specific state are represented by a single prefix that defines a set of current states. Our technique applies to a large class of automata, which can be categorized by simple properties. Then, the problem of pattern matching is reduced to the well-studied problem of Longest Prefix Match (LPM), which can be solved either in ternary content-addressable memory (TCAM), in commercially available IP-lookup chips, or in software. Specifically, we show that with a TCAM our scheme can reach a throughput of 10 Gb/s with low power consumption.
Blockade of Pachytene piRNA Biogenesis Reveals a Novel Requirement for Maintaining Post-Meiotic Germline Genome Integrity

Piwi-interacting RNAs are a diverse class of small non-coding RNAs implicated in the silencing of transposable elements and the safeguarding of genome integrity. In mammals, male germ cells express two genetically and developmentally distinct populations of piRNAs at the pre-pachytene and pachytene stages of meiosis, respectively. Pre-pachytene piRNAs are mostly derived from retrotransposons and required for their silencing. In contrast, pachytene piRNAs originate from ∼3,000 genomic clusters, and their biogenesis and function remain enigmatic. Here, we report that conditional inactivation of the putative RNA helicase MOV10L1 in mouse spermatocytes produces a specific loss of pachytene piRNAs, significant accumulation of pachytene piRNA precursor transcripts, and unusual polar conglomeration of Piwi proteins with mitochondria. Pachytene piRNA–deficient spermatocytes progress through meiosis without derepression of LINE1 retrotransposons, but become arrested at the post-meiotic round spermatid stage with massive DNA damage. Our results demonstrate that MOV10L1 acts upstream of Piwi proteins in the primary processing of pachytene piRNAs and suggest that, distinct from pre-pachytene piRNAs, pachytene piRNAs fulfill a unique function in maintaining post-meiotic genome integrity.
Serum HMGB1 as a Diagnostic Marker for Malignant Peritoneal Mesothelioma

Background: Diffuse malignant peritoneal mesothelioma (DMPM) is an aggressive malignant tumor of mesothelial origin that shows a limited response to cytoreductive surgery along with intraperitoneal chemotherapy. Therefore, early diagnosis of DMPM is very important. Some researchers have previously reported that high-mobility group box 1 (HMGB1) was correlated with pulmonary fibrosis. DMPM involves the malignant transformation of mesothelial cells, which originate from mesenchymal cells, similar to lung fibroblasts. Here, we investigated serum levels of HMGB1 in patients with MPM and compared them with those of a population that had been exposed to asbestos without developing MPM. Study: The serum concentrations of HMGB1 were measured in 13 DMPM patients and 45 individuals with benign asbestos-related diseases. Result: We demonstrated that the patients with DMPM had significantly higher serum levels of HMGB1 compared with the population who had been exposed to asbestos but did not develop DMPM. Conclusion: Our data suggest that serum HMGB1 concentration is a useful serum marker for DMPM.
Trends of summertime extreme temperatures in the Arctic

Extreme temperature events can influence the natural environment and societal activities more so than mean temperature events. This study used daily data from 238 stations north of 60°N, obtained from the Global Summary of the Day dataset for the period 1979–2015, to investigate the trends of summertime extreme temperature. The results revealed most stations north of 60°N with trends of decrease in the number of cold days (nights) and increase in the number of warm days (nights). The regional average results showed trends of consistent decline (rise) of cold days and nights (warm days and nights) in Eurasia and Greenland. Similarly, the trends of the seasonal maximum and minimum values were most significant in these regions. In summer, of three indices considered (i.e., Arctic Oscillation, Arctic dipole, and El Nino–Southern Oscillation), the largest contributor to the trends of extreme temperature events was the Arctic dipole. Prevailing southerly winds in summer brought warm moist air across northern Eurasia and Greenland, conducive to increased numbers of warm days (nights) and decreased numbers of cold day (nights). Moreover, we defined extreme events using different thresholds and found the spatial distributions of the trends were similar.
Host-Pathogen Interactions: Basic Concepts of Microbial Commensalism, Colonization, Infection, and Disease

Most of the terminology used to define the host-microbe interaction has been in use for nearly a century. Early in this period, microbes were thought to be primary aggressors that governed the host-pathogen interaction, resulting in disease. Later, new information about the attributes of microbes and their hosts resulted in the understanding that the hostpathogen interaction does not always result in disease. This recognition, in turn, led to the introduction of terms to explain states in which microbes exist within hosts without causing overt disease and why some microbes only cause disease in certain hosts. Commensal, carrier state, and opportunist were terms put forth to account for microbes and conditions that were sometimes associated with disease but for which Koch’s postulates could not be fulfilled for one reason or another. Most of these terms were originally proposed to describe the behavior of particular microbes, rather than to define a more general host-microbe relationship. Recently, we reviewed the concepts of virulence and pathogenicity and described how the definitions for these terms changed over the years as microbiologists tried to find ways to convey that microbial pathogenesis reflects an interaction between two entities, host and pathogen (7). Based on the concept that host damage was the most relevant outcome of the host-pathogen interaction, we proposed revisions to the definitions of the terms pathogen, pathogenicity, and virulence (7). However, the proposed framework suggested a need to reexamine the terms used to define the outcomes of host-microbe interactions. Here, we critically review the origin and historical evolution of key concepts used to describe the outcome of host-microbe interactions, namely, infection, commensalism, colonization, persistence, infection, and disease. We propose that the meaning of these terms can be clarified by placing them in the context of the damage framework put forth previously (7).