Miracle-dz/UniFAR-FTUs huggingface dataset:
Species Diversity, Community Dynamics, and Metabolite Kinetics of the Microbiota Associated with Traditional Ecuadorian Spontaneous Cocoa Bean Fermentations

ABSTRACT Traditional fermentations of the local Ecuadorian cocoa type Nacional, with its fine flavor, are carried out in boxes and on platforms for a short time. A multiphasic approach, encompassing culture-dependent and -independent microbiological analyses of fermenting cocoa pulp-bean samples, metabolite target analyses of both cocoa pulp and beans, and sensory analysis of chocolates produced from the respective fermented dry beans, was applied for the investigation of the influence of these fermentation practices on the yeast and bacterial species diversity and community dynamics during cocoa bean fermentation. A wide microbial species diversity was found during the first 3 days of all fermentations carried out. The prevailing ethanol-producing yeast species were Pichia kudriavzevii and Pichia manshurica, followed by Saccharomyces cerevisiae. Leuconostoc pseudomesenteroides (glucose and fructose fermenting), Fructobacillus tropaeoli-like (fructose fermenting), and Lactobacillus fermentum (citrate converting, mannitol producing) represented the main lactic acid bacterial species in the fermentations studied, resulting in intensive heterolactate metabolism of the pulp substrates. Tatumella saanichensis and Tatumella punctata were among the members of the family Enterobacteriaceae present during the initial phase of the cocoa bean fermentations and could be responsible for the production of gluconic acid in some cases. Also, a potential new yeast species was isolated, namely, Candida sorbosivorans-like. Acetic acid bacteria, whose main representative was Acetobacter pasteurianus, generally appeared later during fermentation and oxidized ethanol to acetic acid. However, acetic acid bacteria were not always present during the main course of the platform fermentations. All of the data taken together indicated that short box and platform fermentation methods caused incomplete fermentation, which had a serious impact on the quality of the fermented dry cocoa beans.
Adolescents Values Clarification and Development: A Model for Group Counseling

Abstract Youths involved with the juvenile justice and child welfare systems report higher rates of early initiation of sexual intercourse, more sexual partners, and lower rates of condom use compared with the general adolescent population. Such risky behaviors leave system-involved youths with volatile behavioral challenges and negative sexual health outcomes, such as unintended pregnancy. These effects can be attributed to detached support systems and a lack of early interventions, such as group therapy. This dynamic fosters further inquiry into asking, can delinquent teenagers who adopt a values clarification approach and understanding exhibit positive prosocial thoughts and behaviors? The intent of this paper is to discuss an alternative education program for pregnant, delinquent adolescents and young mothers allowed a social worker and his associates to implement a group counseling program. The counseling was intended to emphasize values clarification and values development. The counselors focused on attitudes, social views, and desired behaviors related to values. A unique aspect of the program was the development of a four-phase cognitive process related to values clarification and development. This process includes the discovery and awareness of values, the claiming and reclaiming of values, the acceptance of core values, and the appreciation and advocacy of the values phase. A content analysis methodology was used to analyze a self-report methods so that insights into cultural trends and experiences could be understood. Findings from the adoption of this program suggest a psychoeducation humanistic model can not only buffer teenage pregnancy risk and delinquency but also strengthen values and the moral development of troubled youth.
High performance algorithms for lattice-based cryptanalysis

With quantum-computing, classical cryptosystems, such as RSA, can easily be broken. Today, lattice-based cryptography stands out as one of the most promising and prominent post-quantum type of cryptosystems. The cryptanalysis of new types of cryptography is a crucial part of their development, as it allows one to understand and improve the degree of security of these systems. The same way the security of RSA is deeply connected to the factorization of large integers, the security of lattice-based cryptography revolves around lattice problems such as the Shortest Vector Problem (SVP). While the cryptography community has developed in-depth knowledge of the algorithms that solve these problems (which we also refer to as attacks), from a theoretical point of view, the practical performance of these algorithms is commonly not well understood. In particular, the practical performance of many classes of attacks is not congruent with theoretical expectations. This gap in knowledge is problematic because the security parameters of cryptosystems are selected based on the asymptotic complexity of the available attacks, but only those that are proven to be practical and scalable are considered. Therefore, if some theoretically strong algorithms are erroneously ruled out from this process, because they are believed to be impractical or not scalable, the security parameters of cryptosystems may not be appropriate. In particular, overly strong parameters lead to inefficient cryptosystems, while overly weak parameters render cryptosystems insecure. This is the reason why one must determine the real potential of attacks in practice. The key to understanding is to consider the underlying computer architecture and its influence on the performance of these algorithms, so an effective map between the algorithm and the architecture can be done. This means in particular, to develop appropriate parallelization methods for these algorithms, as all modern computer architectures employ parallel units of various flavours. This thesis aims to fill this gap in knowledge, by describing computational analyses and techniques to parallelize and optimize attacks, with focus on sieving algorithms, in modern, parallel computer architectures. In particular, we show that (i) lattice basis reduction algorithms can benefit largely from cache friendly data structures and scale well, if the right parameters are used, (ii) enumeration algorithms can scale linearly and super-linearly if appropriate mechanisms are employed and (iii) sieving algorithms can be implemented in such a way that very good scalability is achieved, even for high core counts, if the properties of the algorithms are slightly relaxed. Throughout the thesis, we also provide heuristics to enhance the practical performance of specific algorithms, and various optimizations in practice, especially related to memory access.
Flyables: Exploring 3D Interaction Spaces for Levitating Tangibles

Recent advances in technology and miniaturization allow the building of self-levitating tangible interfaces. This includes flying tangibles, which extend the mid-air interaction space from 2D to 3D. While a number of theoretical concepts about interaction with levitating tangibles were previously investigated by various researchers, a user-centered evaluation of the presented interaction modalities has attracted only minor attention from prior research. We present Flyables, a system adjusting flying tangibles in 3D space to enable interaction between users and levitating tangibles. Interaction concepts were evaluated in a user study(N=17), using quadcopters as operable levitating tangibles. Three different interaction modalities are evaluated to collect quantitative data and qualitative feedback. Our findings show preferred user interaction modalities using Flyables. We conclude our work with a discussion and future research within the domain of human-drone interaction.
Impact of Users’ Security Awareness on Desktop Security Behavior: A Protection Motivation Theory Perspective

ABSTRACT This article uses the protection motivation theory to study the impact of information security awareness on desktop security behavior. It contributes to the literature by examining the roles played by awareness, an important antecedent to the cognitive processes in the protection motivation theory. The findings indicate that security awareness significantly affects perceived severity, response efficacy, self-efficacy, and response cost. Constructs in the coping appraisal process (except response cost), in turn, significantly impact recommended security behavior.
T cells are responsible for the enhanced synovial cellular immune response to triggering antigen in reactive arthritis

In reactive arthritis (ReA) there is specific proliferation of synovial fluid (SF) mononuclear cells (MNC) to the triggering bacterial antigen; comparatively little or no response is seen in peripheral blood (PB). To investigate the mechanism of this elevated local immune response, we examined patients with typical ReA who showed an enhanced antigen‐specific synovial immune response in bulk culture. Using separated fractions of T cells and antigen‐presenting cells (APC) from PB and SF we showed that the synovial T cells rather than SF APC are responsible for the specific proliferation. By limiting dilution analysis, the frequency of T cells responding to the specific antigen was found to be significantly increased compared with the frequency of irrelevant antigen‐specific T cells. Furthermore, the frequency of T cells responding to the specific antigen was higher in SF (between 1/619 and 1/4846, mean 1/2389) than in PB (between 1/1286 and 1/16279, mean 1/7350). We conclude that the specific synovial cellular immune response in ReA is mainly due to an expansion of antigen‐specific T cells within the joint. However, the non‐specific hyper‐reactivity of SF T cells and differences between SF and PB APC may make a more minor contribution.
Genome-Wide Convergence during Evolution of Mangroves from Woody Plants

When living organisms independently invade a new environment, the evolution of similar phenotypic traits is often observed. An interesting but contentious issue is whether the underlying molecular biology also converges in the new habitat. Independent invasions of tropical intertidal zones by woody plants, collectively referred to as mangrove trees, represent some dramatic examples. The high salinity, hypoxia, and other stressors in the new habitat might have affected both genomic features and protein structures. Here, we developed a new method for detecting convergence at conservative Sites (CCS) and applied it to the genomic sequences of mangroves. In simulations, the CCS method drastically reduces random convergence at rapidly evolving sites as well as falsely inferred convergence caused by the misinferences of the ancestral character. In mangrove genomes, we estimated ∼400 genes that have experienced convergence over the background level of convergence in the nonmangrove relatives. The convergent genes are enriched in pathways related to stress response and embryo development, which could be important for mangroves' adaptation to the new habitat.
Effect of deletion and overexpression of tryptophan metabolism genes on growth and fermentation capacity at low temperature in wine yeast

Low‐temperature fermentations produce wines with greater aromatic complexity, but the success of these fermentations greatly depends on the adaptation of yeast cells to cold. Tryptophan has been previously reported to be a limiting amino acid during Saccharomyces cerevisiae growth at low temperature. The objective of this study was to determine the influence of the tryptophan metabolism on growth and fermentation performance during low‐temperature wine fermentation. To this end, we constructed the deletion mutants of the TRP1 and TAT2 genes in a derivative haploid of a commercial wine strain, and the TAT2 gene was overexpressed in the prototroph and auxotroph (Δtrp1) backgrounds. Then we characterized growth and fermentation activity during wine fermentation at low and optimum temperatures. Our results partially support the role of this amino acid in cold yeast growth. Although deletion of TRP1 impaired amino acid uptake and the growth rate at low temperature in synthetic must, this growth impairment did not affect the fermentation rate. Deletion of TAT2 endorsed this strain with the highest nitrogen consumption capacity and the greatest fermentation activity at low temperature. Our results also evidenced reduced ammonium consumption in all the strains at low temperature. © 2014 American Institute of Chemical Engineers Biotechnol. Prog. , 30:776–783, 2014
The Role of Identity in Support for Supranational Integration in EU Foreign and Security Policies

This paper examines the effect of popular identification with Europe and the European Union on the level of governments’ willingness to consent to supranational reforms of foreign and security policies. Applying ordinary least squares (OLS) regression on a series of statistical analyses based on data provided by Eurobarometer and state positions prior to the three major EU treaties (the 1992 Maastricht Treaty, the 1997 Amsterdam Treaty and the 2004 Constitutional Treaty), this paper concludes that higher levels of European identification by citizens greatly increase domestic support for joint decision-making in foreign and defence policies which in turn pushes governments to adopt more integrationist positions during negotiations.
Survey: The locked-in syndrome: a syndrome looking for a therapy

The locked-in syndrome (LIS) is a very severe condition caused by a primary vascular or traumatic injury to the brainstem, normally corresponding to a ventral pons lesion due to an obstruction of the basilar artery, and characterized by upper motor neuron quadriplegia, paralysis of lower cranial nerves, bilateral paresis of horizontal gaze and anarthria, and with preserved consciousness. Patients who have suffered this pontine lesion generally have preserved vertical eye movements and movement of the eyelids (blinking), this being their only means of responding to the outside world. A survey was conducted of 44 people diagnosed with LIS, all of them belonging to the Association of Locked-in Syndrome (ALIS) of France. Results of this survey showed that LIS was equally frequent in men and women (51.2% vs. 48.1%) and had occurred at any age between 22-77 years of age (normally between 41-52 years, the mean age being 46.79 years). The average time that transpired post-insult was 71.35 months. The principal cause of LIS was stroke (86.4%), with traumatic brain injury (TBI) being a distant second cause with an incidence of only 13.6%. The diagnosis of LIS was usually made around the middle of the second month after onset (mean of 78.76 days). The principal treatments, when present, were pharmacological and physiotherapy. However, 47.1% of the patients were not receiving treatment of any kind at the time of the survey. Neuropsychologically, 86% had a good attentional level, 97.6% were temporally oriented and 76.7% could read; 18.6% reported memory problems and 24% showed visual deficit (found mainly in patients with LIS originated by TBI); 47.5% reported a good mood state and 12.5% reported feeling depressed; 61.1% reported having sexual desire, but only 30% maintained sexual relations; 78% were capable of emitting sounds and 65.8% could communicate without technical aid; 73.2% enjoyed going out and 81% met with friends at least twice a month. Only 14.3% participated in social activities and 23.8% watched television regularly. Nearly 100% of the patients reported being sensitive to touch to any part of their bodies. This survey suggests diagnostics and rehabilitation procedures.
Laparoscopic repair for perforated peptic ulcer disease.

BACKGROUND Perforated peptic ulcer is a common abdominal disease that is treated by surgery. The development of laparoscopic surgery has changed the way to treat such abdominal surgical emergencies. The results of some clinical trials suggest that laparoscopic surgery could be a better strategy than open surgery in the correction of perforated peptic ulcer but the evidence is not strongly in favour for or against this intervention. OBJECTIVES To measure the effect of laparoscopic surgical treatment versus open surgical treatment in patients with a diagnosis of perforated peptic ulcer in relation to abdominal septic complications, surgical wound infection, extra-abdominal complications, hospital length of stay and direct costs. SEARCH METHODS We searched the Cochrane Central Register of Controlled Trials (CENTRAL) on The Cochrane Library (2004, Issue 2), PubMed/MEDLINE (1966 to July 2004), EMBASE (1985 to November 2004) and LILACS (1988 to November 2004) as well as the reference lists of relevant articles. Searches in all databases were updated in December 2009 and January 2012. We did not confine our search to English language publications. SELECTION CRITERIA Randomized clinical trials comparing laparoscopic surgery versus open surgery for the repair of perforated peptic ulcer using any mechanical method of closure (suture, omental patch or fibrin sealant). DATA COLLECTION AND ANALYSIS Primary outcome measures included proportion of septic and other abdominal complications (surgical site infection, suture leakage, intra-abdominal abscess, postoperative ileus) and extra-abdominal complications (pulmonary). Secondary outcomes included mortality, time to return to normal diet, time of nasogastric aspiration, hospital length-of-stay and costs. Outcomes were summarized by reporting odds ratios (ORs) and 95% confidence intervals (CIs), using the fixed-effect model. MAIN RESULTS We included three randomized clinical trials of acceptable quality. We found no statistically significant differences between laparoscopic and open surgery in the proportion of abdominal septic complications (OR 0.66; 95% CI 0.30 to 1.47), pulmonary complications (OR 0.43; 95% CI 0.17 to 1.12) or number of septic abdominal complications (OR 0.60; 95% CI 0.32 to 1.15). Heterogeneity was significant for pulmonary complications and operating time. AUTHORS' CONCLUSIONS This review suggests that a decrease in septic abdominal complications may exist when laparoscopic surgery is used to correct perforated peptic ulcer. However, it is necessary to perform more randomized controlled trials with a greater number of patients to confirm such an assumption, guaranteeing a long learning curve for participating surgeons. With the information provided it could be said that laparoscopic surgery results are not clinically different from those of open surgery.
Effects of immunization with Cryptococcus neoformans cells or cryptococcal culture filtrate antigen on direct anticryptococcal activities of murine T lymphocytes

Immunizing CBA/J mice with intact Cryptococcus neoformans cells or with a cryptococcal culture filtrate antigen (CneF) induces an anticryptococcal delayed-type hypersensitivity response. Recently, it has been shown that two phenotypically different T-cell populations are responsible for delayed-type hypersensitivity reactivity in mice immunized with intact cryptococcal cells, whereas only one of those populations is present in mice immunized with soluble cryptococcal antigens in complete Freund's adjuvant (CFA). The purpose of this study was to determine if differences occur with regard to direct anticryptococcal activity between T-lymphocyte-enriched populations from mice immunized with intact viable or dead cryptococcal cells and similar cell populations from mice immunized with the soluble cryptococcal culture filtrate antigen, CneF, emulsified in CFA. The percentage of lymphocytes which form conjugates with C. neoformans and the percentage of cryptococcal growth inhibition in vitro are greater with T-lymphocyte-enriched populations from mice sublethally infected with C. neoformans or from mice immunized with intact heat-killed cryptococcal cells in the presence or absence of CFA than with lymphocyte populations from mice immunized with CneF-CFA. Enhanced anticryptococcal activity of T lymphocytes could be induced by immunizing mice with heat-killed C. neoformans cells of serotype A, B, C, or D as well as by immunizing with a similar preparation of an acapsular C. neoformans mutant but not by immunizing with CFA emulsified with CneF prepared from any one of the C. neoformans isolates. These data indicate that the soluble cryptococcal culture filtrate antigens do not induce the same array of functional T lymphocytes as whole cryptococcal cells.
Effects of Rosemary (Rosmarinus officinalis) on Lipid Profile of Diabetic Rats

The purpose of this study was to determine the hypoglycemic activity of the aqueous extract perfusion of rosemary (Rosmarinus officinalis Linn.) in normal and streptozotocin-induced diabetic rats. The sugar level and lipid profile were investigated in plasma of normal and streptozotocin-induced diabetic rats treated with rosemary for four weeks. Diabetic rats exhibited an increase in the levels of sugar, total cholesterol, triglycerides and low density lipoprotein cholesterol (LDLcholesterol), and a decrease in the level of high density lipoprotein cholesterol (HDL-cholesterol). The administration of rosemary shows a decrease by 20% in sugar level, 22% in total cholesterol, 24% triglycerides, and by 27% in LDLcholesterol, and an increase by 18% in HDL-cholesterol. The findings of this study indicate that the administration of rosemary resulted in a better lipid profile and decreased blood sugar level in both normal and diabetic rats.
SPITZER OBSERVATIONS OF THE λ ORIONIS CLUSTER. II. DISKS AROUND SOLAR-TYPE AND LOW-MASS STARS

We present IRAC/MIPS Spitzer Space Telescope observations of the solar-type and the low-mass stellar population of the young (∼5 Myr) λ Orionis cluster. Combining optical and Two Micron All Sky Survey photometry, we identify 436 stars as probable members of the cluster. Given the distance (450 pc) and the age of the cluster, our sample ranges in mass from 2 M☉ to objects below the substellar limit. With the addition of the Spitzer mid-infrared data, we have identified 49 stars bearing disks in the stellar cluster. Using spectral energy distribution slopes, we place objects in several classes: non-excess stars (diskless), stars with optically thick disks, stars with “evolved disks” (with smaller excesses than optically thick disk systems), and “transitional disk” candidates (in which the inner disk is partially or fully cleared). The disk fraction depends on the stellar mass, ranging from ∼6% for K-type stars (RC − J < 2) to ∼27% for stars with spectral-type M5 or later (RC − J>4). We confirm the dependence of disk fraction on stellar mass in this age range found in other studies. Regarding clustering levels, the overall fraction of disks in the λ Orionis cluster is similar to those reported in other stellar groups with ages normally quoted as ∼5 Myr.