Miracle-dz/UniFAR-FTUs huggingface dataset:
Working Papers Maternal Employment , Migration , and Child Development

We use longitudinal models to investigate the interactions and interdependencies between parental inputs and school inputs as determinants of a child’s development. Using data from the National Longitudinal Survey of Youth, we integrate information on household migration, maternal employment decisions, and the mother’s wage rate with observations on child outcomes for 7184 persons over 10 years. A mother maximizes her utility that depends on the household’s consumption, her “leisure” time, and her child’s achievement outcome. The mother solves a stochastic optimization problem where she is uncertain of her future wages and job prospects. She can only imperfectly influence her child’s development. We use semi-parametric maximum likelihood procedures to estimate the structure of her preferences and the stochastic child production process under the assumption that the mother maximizes her expected utility. The statistical model follows directly from the theoretical framework. We relax many functional form assumptions that have been imposed by previous researchers who have studied how parents and schools can affect a child’s development. Our preliminary investigations with simplified versions of this approach indicate that we are able to explain and reject several of the counter-intuitive estimation results found in the literature on the determinants of children’s school performance.
The protection role of heat shock protein 70 (HSP-70) in the testes of cadmium-exposed rats

Cadmium (Cd) is an environmental carcinogenic pollutant known to inactivate several proteins involved in DNA repair systems while at the same time creating an oxidative stress that can result in additional DNA lesions. The testis and the lung are the target organs for cadmium carcinogenesis. Increased production of oxidants in vivo can cause damage to intracellular macromolecules such as DNA, proteins and lipids, which in turn lead to oxidative injury. So, this investigation aimed to evaluate the protective role of L-Carnitine through up regulation of HSPs against DNA damage induced by cadmium chloride. The current study was carried out on forty adult male rats, each with average weight 220-250g. , were divided into 4 equal groups. 1st group was received saline solution (0.5 ml/100 g body weight) and kept as control. 2nd group was received 500mg / kg body weight L-Carnitine intraperitoneally (IP). 3rd group was administered 1.2 mg cadmium chloride IP. 4th group was received both cadmium chloride and L-Carnitine simultaneously. The comet assay parameters showed significantly increased HSP70 and DNA damage in testis cells after 10 and 56 days in the third group. Meanwhile, HSP70 showed significantly decreased levels after 10 days and 56 days in the fourth group after L-Carnitine treatment simultaneously with cadmium chloride. The results of the present study demonstrate a damaging effect of cadmium chloride on DNA of the testis cells (with low stress response). This damaging effect increases the synthesis of HSP70 that upregulated by L-Carnitine treatment and showed ameliorative effect of the cells for recovery.
Enzymatically Produced Pools of Canonical and Dicer-Substrate siRNA Molecules Display Comparable Gene Silencing and Antiviral Activities against Herpes Simplex Virus

RNA interference (RNAi)-based sequence-specific gene silencing is applied to identify gene function and also possesses great potential for inhibiting virus replication both in animals and plants. Small interfering RNA (siRNA) molecules are the inducers of gene silencing in the RNAi pathway but may also display immunostimulatory activities and promote apoptosis. Canonical siRNAs are 21 nucleotides (nt) in length and are loaded to the RNA Induced Silencing Complex when introduced into the cells, while longer siRNA molecules are first processed by endogenous Dicer and thus termed Dicer-substrate siRNA (DsiRNA). We have applied RNA polymerases from bacteriophages T7 and phi6 to make high-quality double-stranded RNA molecules that are specific for the UL29 gene of herpes simplex virus (HSV). The 653 nt long double-stranded RNA molecules were converted to siRNA and DsiRNA pools using Dicer enzymes originating from human or Giardia intestinalis, producing siRNAs of approximately 21 and 27 nt in length, respectively. Chemically synthesised 21 and 27 nt single-site siRNA targeting the UL29 were used as references. The impact of these siRNAs on cell viability, inflammatory responses, gene silencing, and anti-HSV activity were assayed in cells derived from human nervous system and skin. Both pools and the canonical single-site siRNAs displayed substantial antiviral activity resulting in four orders of magnitude reduction in virus titer. Notably, the pool of DsiRNAs caused lower immunostimulation than the pool of canonical siRNAs, whereas the immunostimulation effect was in relation to the length with the single-site siRNAs. Our results also propose differences in the processivity of the two Dicers.
The Evolution of Domain-General Mechanisms in Intelligence and Learning

For both humans and animals, domain-general mechanisms are fallible but powerful tools for attaining evolutionary goals (e.g., resources) in uncertain, novel environments that were not recurrent features of the environment of evolutionary adaptedness. Domain-general mechanisms interact in complex ways with domain-specific, information-encapsulated modules, most importantly by manipulating information obtained from various modules in attempting to solve novel problems. Mechanisms of general intelligence, particularly the executive functions of working memory, underlie analogical reasoning as well as the decontextualization processes that are central to human thought. Although there is a variety of evolved, special purpose learning devices, learning is also characterized by domain-general mechanisms that are able to achieve evolutionary goals by making novel and serendipitous associations with environmental cues.
Epidemiological typing of Bacillus spp. isolated from food

Biotypes, fatty acid profiles, and restriction fragment length polymorphisms of a PCR product (PCR-RFLP of the cereolysin AB gene) were compared for 62 isolates of the Bacillus cereus group. Eleven isolates originated from various foods, and 51 isolates were obtained from pasteurized milk which had been processed by two different dairies. The isolates were clustered into 6 biotypes, 10 fatty acid groups, or 7 PCR-RFLP clusters. Isolates with mesophilic or psychrotrophic characteristics were preferentially distributed into specific fatty acid or PCR-RFLP groups (P = 0.004). Unique fatty acid clusters were predominantly found in milk samples of each dairy (P < 0.0001), suggesting that certain dairy plants may harbor plant-specific B. cereus which might constantly contribute to postpasteurization contamination.
Embedded Empathy in Continuous, Interactive Health Assessment

As an increasing number of new technologies are turning a strong focus on health assessment applications, new engineering and design challenges emerge. Challenges such as inference, modeling, data mining, and feedback for long-term usage arise. This paper argues that embedding empathy into the design of these interactive systems can potentially be vital in the acceptance and success of these types of technologies. This paper discusses three pieces of work that illustrate that designing systems that are intentionally empathetic can play a significant role in creating a better user experience in human-computer interactions.
Report on Pairing-based Cryptography

This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST’s position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed.
Pleistocene isolation and recent gene flow in Haliotis asinina, an Indo‐Pacific vetigastropod with limited dispersal capacity

Haliotis asinina is a broadcast‐spawning mollusc that inhabits Indo‐Pacific coral reefs. This tropical abalone develops through a nonfeeding larval stage that is competent to settle on specific species of coralline algae after 3–4 days in the plankton. Failure to contact an inductive algae within 10 days of hatching usually results in death. These life cycle characteristics suggest a limited capacity for dispersal and thus gene flow. This makes H. asinina particularly suitable for elucidating phylogeographical structure throughout the Indo‐Malay Archipelagoes, and eastern Indian and western Pacific Oceans, all regions of biogeographical complexity and high conservation value. We assayed 482 bp of the mitochondrial cytochrome oxidase II gene in 206 abalone collected from 16 geographically discrete sites across the Indian and Pacific Oceans and Indo‐Malay Archipelagoes. DNA sequence variation was analysed via population genetics and phylogenetics, and by nested clade analyses (NCA). Our data resolved clear phylogeographical breaks among major biogeographical regions, with sequence divergences ranging from a high of 3.7% and 3.0% between Indian and Pacific sites and Pacific and Indo‐Malay sites, respectively, to a low of 1.1% between Indian and Indo‐Malay sites. Despite the apparent limited dispersal capacity of H. asinina, no finer scale phylogeographical structure was resolved within the respective biogeographical regions. However, amova and NCA identified several significant associations between haplotypes and geographical distribution, most notably higher gene flow among geographical populations associated with major ocean currents. Our study provides further evidence that larval dispersal capacity alone is not a good predictor of population genetic structure in marine invertebrates. We infer instead that a combination of historical events (long–term barriers followed by range expansion associated with Pleistocene sea level changes) and contemporary processes (gene flow restricted by life history and oceanography) have shaped observed patterns of H. asinina phylogeography.
The Orthopoxvirus 68-Kilodalton Ankyrin-Like Protein Is Essential for DNA Replication and Complete Gene Expression of Modified Vaccinia Virus Ankara in Nonpermissive Human and Murine Cells

ABSTRACT Modified vaccinia virus Ankara (MVA) is a highly attenuated and replication-deficient vaccinia virus (VACV) that is being evaluated as replacement smallpox vaccine and candidate viral vector. MVA lacks many genes associated with virulence and/or regulation of virus tropism. The 68-kDa ankyrin-like protein (68k-ank) is the only ankyrin repeat-containing protein that is encoded by the MVA genome and is highly conserved throughout the Orthopoxvirus genus. We showed previously that 68k-ank is composed of ankyrin repeats and an F-box-like domain and forms an SCF ubiquitin ligase complex together with the cellular proteins Skp1a and Cullin-1. We now report that 68k-ank (MVA open reading frame 186R) is an essential factor for completion of the MVA intracellular life cycle in nonpermissive human and murine cells. Infection of mouse NIH 3T3 and human HaCaT cells with MVA with a deletion of the 68k-ank gene (MVA-Δ68k-ank) was characterized by an extensive reduction of viral intermediate RNA and protein, as well as late transcripts and drastically impaired late protein synthesis. Furthermore, infections with MVA-Δ68k-ank failed to induce the host protein shutoff that is characteristic of VACV infections. Although we demonstrated that proteasome function in general is essential for the completion of the MVA molecular life cycle, we found that a mutant 68k-ank protein with a deletion of the F-box-like domain was able to fully complement the deficiency of MVA-Δ68k-ank to express all classes of viral genes. Thus, our data demonstrate that the 68k-ank protein contains another critical domain that may function independently of SCF ubiquitin ligase complex formation, suggesting multiple activities of this interesting regulatory protein.
Pressure Inactivation of Bacillus Endospores

ABSTRACT The inactivation of bacterial endospores by hydrostatic pressure requires the combined application of heat and pressure. We have determined the resistance of spores of 14 food isolates and 5 laboratory strains of Bacillus subtilis, B. amyloliquefaciens, and B. licheniformis to treatments with pressure and temperature (200 to 800 MPa and 60 to 80°C) in mashed carrots. A large variation in the pressure resistance of spores was observed, and their reduction by treatments with 800 MPa and 70°C for 4 min ranged from more than 6 log units to no reduction. The sporulation conditions further influenced their pressure resistance. The loss of dipicolinic acid (DPA) from spores that varied in their pressure resistance was determined, and spore sublethal injury was assessed by determination of the detection times for individual spores. Treatment of spores with pressure and temperature resulted in DPA-free, phase-bright spores. These spores were sensitive to moderate heat and exhibited strongly increased detection times as judged by the time required for single spores to grow to visible turbidity of the growth medium. The role of DPA in heat and pressure resistance was further substantiated by the use of the DPA-deficient mutant strain B. subtilis CIP 76.26. Taken together, these results indicate that inactivation of spores by combined pressure and temperature processing is achieved by a two-stage mechanism that does not involve germination. At a pressure between 600 and 800 MPa and a temperature greater than 60°C, DPA is released predominantly by a physicochemical rather than a physiological process, and the DPA-free spores are inactivated by moderate heat independent of the pressure level. Relevant target organisms for pressure and temperature treatment of foods are proposed, namely, strains of B. amyloliquefaciens, which form highly pressure-resistant spores.
Long-term outcomes of neoadjuvant chemotherapy followed by concurrent chemoradiotherapy (CCRT) vs CCRT alone for nasopharyngeal carcinoma in the era of intensity-modulated radiation therapy using propensity score matching method

Purpose Whether neoadjuvant chemotherapy (NCT) followed by concurrent chemoradiotherapy (CCRT) could improve survival in nasopharyngeal carcinoma (NPC) remains controversial especially in the era of intensity-modulated radiation therapy (IMRT), and we explored the role of NCT for NPC patients. Patients and methods A retrospective review was conducted of 255 NPC patients treated with NCT+CCRT (n=67) or CCRT alone (n=188) based on IMRT between December 2006 and December 2012. To control the imbalance, a 1:2 match was performed using propensity score matching (PSM) method based on patient’s heterogeneity and regimens of concurrent chemotherapy (CCT). The long-term treatment outcomes and toxicity between NCT group (n=67) and concurrent chemoradiotherapy (CRT) group (n=134) after PSM were compared. Results The 5-year overall survival (OS), progression-free survival (PFS), recurrence-free survival (RFS), local recurrence-free survival (LRFS), regional recurrence-free survival (RRFS) and distant failure-free survival (DFFS) were 78.8%, 69.1%, 90.0%, 90.0%, 100% and 78.3% for NCT group, while 79.5%, 75.7%, 92.7%, 94.2%, 96.1% and 82.7% for CRT group (P=0.305, 0.448, 0.790, 0.512, 0.104 and 0.671). It indicated that the treatment method (NCT+CCRT vs CCRT) was not the independent prognostic factor for the survival in NPC patients, and only patients who had completed at least two cycles of CCT got better OS, RFS and DFFS (P=0.009, 0.016 and 0.043), whether to receive NCT or not. No difference in the incidences of any acute and most late toxicity between the two groups was shown. Conclusion Our study did not show the exact advantage of NCT followed by CCRT compared with CCRT alone or higher incidences of toxicity in NCT group. It suggests that NCT might not be necessary if two or more cycles of CCT are finished well in the era of IMRT, and when NCT is finished well, less than two cycles of CCT with IMRT could be enough. However, in the era of IMRT, the role of NCT still needs to be further explored.
Genetic Draft and Quasi-Neutrality in Large Facultatively Sexual Populations

Large populations may contain numerous simultaneously segregating polymorphisms subject to natural selection. Since selection acts on individuals whose fitness depends on many loci, different loci affect each other’s dynamics. This leads to stochastic fluctuations of allele frequencies above and beyond genetic drift—an effect known as genetic draft. Since recombination disrupts associations between alleles, draft is strong when recombination is rare. Here, we study a facultatively outcrossing population in a regime where the frequency of outcrossing and recombination, r, is small compared to the characteristic scale of fitness differences σ. In this regime, fit genotypes expand clonally, leading to large fluctuations in the number of recombinant offspring genotypes. The power law tail in the distribution of the latter makes it impossible to capture the dynamics of draft by an effective neutral model. Instead, we find that the fixation time of a neutral allele increases only slowly with the population size but depends sensitively on the ratio r/σ. The efficacy of selection is reduced dramatically and alleles behave “quasi-neutrally” even for Ns≫1, provided that |s| < sc, where sc depends strongly on r/σ, but only weakly on population size N. In addition, the anomalous fluctuations due to draft change the spectrum of (quasi)-neutral alleles from f(ν) ∼ ν−1, corresponding to drift, to ∼ ν−2. Finally, draft accelerates the rate of two-step adaptations through deleterious intermediates.
The treatment of patients with mycotoxin-induced disease

Twenty-eight incapacitated individuals (average 43 years old, 7 males, 21 females, range 12-70) exposed to molds and mycotoxins were studied and treated with a protocol of cleaning up or changing their environment to be mold free. Injections of the optimum dose of antigens were given as part of the treatment protocol as was oral and intravenous (i.v.) antioxidants; heat depuration (sauna); physical therapy with massage and exercise under environmentally controlled conditions; oxygen therapy at 4-8 L/min for 2 hours with a special wood-grade cellophane reservoir and a glass oxygen container. Many patients were sensitive to plastics; therefore, exposures to these were kept to a minimum. Autogenous lymphocytic factor was given as an immune modulator. Of 28 patients, 27 did well and returned to work. One patient improved but did not return to work during the period of study.
Predictors of Engagement and Participation in an On-Line Course

The use of online learning materials is increasing in both academic and industrial training settings. While the advantages of online learning are exciting and numerous, the problems associated with successful implementation of an online learning program can detract from the educational experience of even the most motivated student. These problems include such factors as poor attendance, procrastination, feelings of isolation, and a general lack of structure in the course (Brown, 2001; Kulik, 1991; Fishman, 1999; Oliver, 1999; Olugbemiro et al., 1999; Young-Ju Joo et al., 2000, Wang and Newlin, 2000). These problems can limit the amount of participation and engagement with the course materials that are offered in the online environment.
Undecidability of the unification and admissibility problems for modal and description logics

We show that the unification problem “is there a substitution instance of a given formula that is provable in a given logic? ” is undecidable for basic modal logics K and K4 extended with the universal modality. It follows that the admissibility problem for inference rules is undecidable for these logics as well. These are the first examples of standard decidable modal logics for which the unification and admissibility problems are undecidable. We also prove undecidability of the unification and admissibility problems for K and K4 with at least two modal operators and nominals (instead of the universal modality), thereby showing that these problems are undecidable for basic hybrid logics. Recently, unification has been introduced as an important reasoning service for description logics. The undecidability proof for K with nominals can be used to show the undecidability of unification for Boolean description logics with nominals (such as ALCO and SHIQO). The undecidability proof for K with the universal modality can be used to show that the unification problem relative to role boxes is undecidable for Boolean description logics with transitive roles, inverse roles, and role hierarchies (such as SHI and SHIQ).
Genetic Aberrations Leading to MAPK Pathway Activation Mediate Oncogene-Induced Senescence in Sporadic Pilocytic Astrocytomas

Purpose: Oncogenic BRAF/Ras or NF1 loss can potentially trigger oncogene-induced senescence (OIS) through activation of the mitogen-activated protein kinase (MAPK) pathway. Somatic genetic abnormalities affecting this pathway occur in the majority of pilocytic astrocytomas (PA), the most prevalent brain neoplasm in children. We investigated whether OIS is induced in PA. Experimental Design: We tested expression of established senescence markers in three independent cohorts of sporadic PA. We also assessed for OIS in vitro, using forced expression of wild-type and V600E-mutant BRAF in two astrocytic cell lines: human telomerase reverse transcriptase (hTERT)-immortalized astrocytes and fetal astrocytes. Results: Our results indicate that PAs are senescent as evidenced by marked senescence-associated acidic β-galactosidase activity, low KI-67 index, and induction of p16INK4a but not p53 in the majority of 52 PA samples (46 of 52; 88.5%). Overexpression of a number of senescence-associated genes [CDKN2A (p16), CDKN1A (p21), CEBPB, GADD45A, and IGFBP7] was shown at the mRNA level in two independent PA tumor series. In vitro, sustained activation of wild-type or mutant BRAF induced OIS in both astrocytic cell lines. Loss of p16INK4a in immortalized astrocytes abrogated OIS, indicative of the role of this pathway in mediating this phenomenon in astrocytes. OIS is a mechanism of tumor suppression that restricts the progression of benign tumors. We show that it is triggered in PAs through p16INK4a pathway induction following aberrant MAPK activation. Conclusions: OIS may account for the slow growth pattern in PA, the lack of progression to higher-grade astrocytomas, and the high overall survival of affected patients. Clin Cancer Res; 17(14); 4650–60. ©2011 AACR.