Miracle-dz/UniFAR-FTUs huggingface dataset:
Completion of the Genome Sequence of Brucella abortus and Comparison to the Highly Similar Genomes of Brucella melitensis and Brucella suis

ABSTRACT Brucellosis is a worldwide disease of humans and livestock that is caused by a number of very closely related classical Brucella species in the alpha-2 subdivision of the Proteobacteria. We report the complete genome sequence of Brucella abortus field isolate 9-941 and compare it to those of Brucella suis 1330 and Brucella melitensis 16 M. The genomes of these Brucella species are strikingly similar, with nearly identical genetic content and gene organization. However, a number of insertion-deletion events and several polymorphic regions encoding putative outer membrane proteins were identified among the genomes. Several fragments previously identified as unique to either B. suis or B. melitensis were present in the B. abortus genome. Even though several fragments were shared between only B. abortus and B. suis, B. abortus shared more fragments and had fewer nucleotide polymorphisms with B. melitensis than B. suis. The complete genomic sequence of B. abortus provides an important resource for further investigations into determinants of the pathogenicity and virulence phenotypes of these bacteria.
An experimental study on combining Euclidean distances

Combining different distance matrices or dissimilarity representations can often increase the performance of individual ones. In this work, we experimentally study on the performance of combining Euclidean distances and its relationship with the non-Euclideaness produced from combining Euclidean distances. The relationship between the degree of non-Euclideaness from combining Euclidean distances and the correlations between these Euclidean distances are also investigated in the experiments. From the results, we observe that combining dissimilarities computed with Euclidean distances usually performs better than combining dissimilarities computed with squared Euclidean distances. Also, the improvements are found to be highly related to the degree of non-Euclideaness. Moreover, the degree of non-Euclideaness is relatively large if two highly uncorrelated dissimilarity matrices are combined and the degree of non-Euclideaness remains lower if two dissimilarity matrices to be combined are more correlated.
TM 2015 -- Topic Models: Post-Processing and Applications Workshop

The main objective of the workshop is to bring together researchers who are interested in applications of topic models and improving their output. Our goal is to create a broad platform for researchers to share ideas that could improve the usability and interpretation of topic models. We expect this will promote topic model applications in other research areas, making their use more effective.
Nonlinear dynamic process monitoring based on kernel partial least squares

Nonlinearity and dynamic are two typical behaviors that widely present in industrial processes. The monitoring performance of multivariable statistical process control techniques will be degraded if those two behaviors are not well addressed. In this paper, a kernel partial least squares (KPLS) based nonlinear state space model is proposed to model the process, which can handle the nonlinear and dynamic data behaviors simultaneously. Due to the non-Gaussian distribution of the nonlinear scores in the KPLS model, support vector data description is introduced for modeling and the corresponding statistic is constructed for monitoring. Two case studies are provided for performance evaluation of the proposed method.
Coffee Consumption and Heart Rate Variability: The Brazilian Longitudinal Study of Adult Health (ELSA-Brasil) Cohort Study

Studies have shown that acute coffee ingestion can affect cardiovascular autonomic activity, although the chronic effects on heart rate variability (HRV) remain controversial. Method: A cross-sectional study with baseline data (2008–2010) from ELSA-Brasil cohort of 15,105 (aged 35–74), based in six Brazilian states. Coffee consumption in the previous 12 months was measured using the semi-quantitative food frequency questionnaire, and HRV was obtained through electrocardiographic tracings during 10 min at rest. Independent association between the frequency of coffee consumption “never or almost never”, “≤1 cup/day”, “2–3 cups/day”, “≥3 cups/day”, and HRV was estimated using generalized linear regression, adjusting for socio-demographic characteristics, health-related behavior, markers of abnormal metabolism, and the presence of coronary artery disease. Further, we applied Bonferroni correction in the full models. Results: The mean age was 52 years (standard deviation (SD) = 9.1), and 52% was female; 9.5% never/almost never consumed coffee. In univariate analysis, coffee consumers had reduced values of HRV indexes, but after full adjustments and correction for multiple comparisons, these associations disappeared. A trend of reduction in HRV vagal indexes was observed in those that consumed ≥3 cups of coffee/day. Conclusion: Most of the effects attributed to the chronic use of coffee on the HRV indexes is related to the higher prevalence of unhealthy habits in coffee users, such as smoking and alcohol use. Adjustment for confounding factors weaken this association, making it non-significant. The effect of higher daily doses of coffee on the autonomic system should be evaluated in further studies.
Infant temperament, maternal attributions, mood and rumination, in predicting maternal problem-solving and mother-infant bonding in the postnatal period

Background: The present study considers some of the underlying mechanisms that may be acting in postnatal depression (PND). It has been suggested that rumination predicts problem solving ability and that child temperament and maternal attributions predict mother-infant bonding. This study aims to investigate the role that brooding and reflective rumination may play in predicting and mediating these relationships in postnatal women. Methods: Postnatal women were recruited to complete an online survey.190 women responded and completed the Edinburgh Postnatal Depression Scale (EPDS), Maternal Attribution Scale (MAS), Postpartum Bonding Questionnaire (PBQ), Parental Problem Solving Task (PPST), Rumination Response Scale (RRS), Infant Behaviour Questionnaire (IBQ) and a confidence in problem solving using a Visual Analogue Scale (VAS). Results: Analyses showed that reflective rumination mediated the relationship between low infant soothability and high negative attributions, on maternal problem solving. Reflective and Brooding Rumination also predicted confidence in problem solving and mother-infant bonding. Analyses showed that infant temperament (soothability and distress) and maternal attributions (positive and negative) predicted confidence in problem solving and mother-infant bonding Limitations: This study employed a correlational design and therefore all inferences regarding possible causal pathways are tentative. Limitations include the use of self report measures to assess mother-infant bonding and infant temperament. Additionally the PPST is a new measure which needs further validation. Conclusions: Reflective rumination may act as an adaptive strategy for women in the postnatal period when faced with difficult child temperaments, and for those employing negative attributions, when faced with parent specific problem solving tasks. In addition, Brooding and Reflective Rumination may be important in predicting difficulties in mother-infant bonding. Difficult Infant temperaments and less positive or more negative maternal attributions, may affect problem solving, confidence in problem solving and mother-infant bonding in the postnatal period. Future research should look to replicate these findings and explicate possible causal relationships within a postnatal population.
Bosonic Open Strings in a Tachyonic Background Field

We study a bosonic open string coupled to a tachyonic background field $T[X]$ and find that the tachyon field can effectively be replaced by a configuration of D-branes placed at either the zeros or the critical points of $T[X]$, depending on our choice of boundary conditions. This dual picture of the open string tachyon is explored in detail for the explicit case when the tachyonic field is quadratic.
Performance Appraisal: Alternative Perspectives

1. Performance Appraisal and Research Perspectives. 2. Study Type: Laboratory versus Field. 3. Criteria: Error, Accuracy and Qualitative Measures. 4. Rating Formats and Cognitive Processes in Appraisal. 5. Influences on Ratings: Cold and Hot Processing. 6. Person and System Approaches to Appraisal. 7. Sources of Ratings. 8. Basis for Appraisal: Rational and Political. 9. Summary and Concluding Comments.
Hemodilution and hypertension effects on cerebral hemorrhage in cerebral ischemia in rats.

We determined the effect of hemodilution and hypertension on cerebral hemorrhage and brain injury in 32 rats subjected to 180 minutes of middle cerebral artery occlusion and 120 minutes of reperfusion. We divided the rats into four groups. In the control group (n = 8) neither hematocrit nor blood pressure was manipulated during occlusion, in the hemodilution group (n = 8) 5% albumin was administered to maintain a hematocrit of 30% during occlusion, in the hypertension group (n = 8) mean arterial blood pressure was increased to 30 mm Hg above baseline during occlusion with phenylephrine, and in the hemodilution/hypertension group (n = 8) albumin and phenylephrine were employed simultaneously during occlusion. We assessed the amount of cerebral hemorrhage (as concentration of extravasated hemoglobin) spectrophotometrically and the extent of ischemic injury (as percentage of the hemisphere with deficient staining) histochemically using 2,3,5-triphenyltetrazolium chloride. Mean +/- SD hemoglobin concentration in the hemisphere ipsilateral to the occlusion in the hemodilution/hypertension group (71 +/- 14 micrograms/g brain tissue) was significantly (p less than 0.05) greater than that in the hemodilution and hypertension groups (25 +/- 5 and 29 +/- 7 micrograms/g, respectively), hemoglobin concentrations in these two groups were in turn significantly (p less than 0.05) greater than that in the control group (2 +/- 3 micrograms/g). Mean +/- SD percentage of the ipsilateral hemisphere with deficient staining was significantly (p less than 0.05) less in the hypertension and hemodilution hypertension groups (8 +/- 3% and 11 +/- 6%, respectively) than in the control and hemodilution groups (26 +/- 8% and 26 +/- 7%, respectively). (ABSTRACT TRUNCATED AT 250 WORDS)
Social support in patients with anorexia nervosa and bulimia nervosa.

OBJECTIVE To investigate the social support networks of patients with anorexia nervosa (AN) and bulimia nervosa (BN). METHOD Social support was measured using the Significant Others Scale for 44 patients with AN, 81 patients with BN, and 86 polytechnic students. RESULTS Eating disorder patients had smaller social networks than the students. AN patients were significantly less likely than BN patients to have a spouse or partner as a support figure. Both AN and BN patients reported less actual emotional and practical support than students. AN patients perceived their social support to be adequate, whereas BN patients were dissatisfied with their support. Patients set lower ideals for support than the students. Social support was not correlated with duration of illness. DISCUSSION AN and BN patients have deficient social networks. In BN patients there is disturbance in both the size and perceived adequacy of social relationships.
An in vitro investigation into the role of bone marrow-derived mesenchymal stem cells in the control of disc degeneration

Excessive apoptosis and high expression levels of interleukin-1β (IL-1β) in disc cells have been reported to serve important roles in intervertebral disc degeneration (IVDD). Previous studies investigating mesenchymal stem cells (MSCs) have indicated potential for their use in the treatment of IVDD. However, the therapeutic potential and anti-apoptotic ability of MSCs remains to be fully elucidated. The present study aimed to establish an in vitro model for bone marrow-derived MSC (BMSC) therapy by investigating the anti-apoptotic effects, in addition to the migration of BMSCs to nucleus pulposus (NP) cells stimulated by IL-1β. A co-culture system of BMSCs and NP cells was founded. Following inflammatory stimulation, the NP cells exhibited increased indexes for inflammation-induced degeneration. The degenerative and apoptotic indexes were significantly reduced when NP cells were co-cultured with BMSCs. Compared with the indirect co-culture group, the direct co-culture group exhibited an improved capacity for anti-apoptosis. In addition, IL-1β-stimulated NP cells attracted and mediated the migration of BMSCs. Mitochondrial transfer from BMSCs to NP cells by tunneling nanotubes was also observed. In conclusion, the anti-apoptosis and the migration, in addition to mitochondrial transfer associated with BMSC treatments in IVDD, were investigated in vitro in the present study. The interaction between stimulated NP cells and BMSCs is likely involved in to simulating the in vivo process of stem cell-mediated repair.
General anaesthesia vs. spinal anaesthesia for total hip arthroplasty

Sir, We welcome the debate initiated by Dr Peterson et al. focusing on the issue of antimicrobial prophylaxis and resistance in the critically ill requiring treatment on the intensive care unit (ICU). They acknowledge their use of peri-operative antibiotic prophylaxis, but they are opposed to the same application for pneumonia prophylaxis. We assume that the reason is that the use antibiotic prophylaxis to prevent wound infections does not cause resistance, and pneumonia prophylaxis does. We respectfully disagree. Critically ill patients who require treatment on the ICU following liver transplantation show surveillance cultures positive for aerobic Gram-negative bacilli resistant to the parenteral antimicrobial prophylaxis. This is not the case if enteral antimicrobials polymyxin E and tobramycin are added to the parenteral antimicrobials. This observation can be explained by the pathophysiological phenomenon of gut overgrowth, defined as ≥ 10 bacteria per gram of faeces and invariably present in the critically ill. Dr Peterson et al. find the prophylactic use of polymyxin E specifically cumbersome, a statement that is remarkable. A possible explanation may be that the Swedish investigators are unfamiliar with surveillance cultures. Gut overgrowth is associated with resistance following polyclonality due to hypermutation. We thank Dr Peterson et al. for their constructive contribution.
Body Mass Index (BMI) Trajectories from Birth to 11.5 Years: Relation to Early Life Food Intake

Recent research has shown that the pattern of change over time, or trajectory, of body mass index (BMI) varies among children. However, the factors that underlie the heterogeneity in these trajectories remain largely unexplored. Our aim was to use a growth mixture model to empirically identify classes of BMI trajectories (from birth to 11.5 years) and examine the effects of breastfeeding, introduction of solids, as well as food and nutrient intake at 18 months on these BMI trajectories. We identified three BMI growth trajectories between birth and age 11.5 years, separately in boys and girls. Breastfeeding duration less than six months and the early introduction of solids did not adversely influence BMI trajectories in our sample but high intakes of meat, particularly high fat varieties, and high intakes of carbohydrate at age around 18 months were associated with a high BMI trajectory in boys. It is not clear whether these dietary factors confer a direct risk of higher BMI in childhood or are markers for other dietary patterns that are present early and/or develop through childhood and contribute to higher BMI.
Sociodemographic context of the AIDS epidemic in a rural area in Tanzania with a focus on people's mobility and marriage

This analysis focuses on how sociocultural and economic characteristics of a poor semi-urban and rural population (Kisesa ward) in north west Tanzania may directly and indirectly affect the epidemiology of HIV and other sexually transmitted infections (STI). Poverty and sociocultural changes may contribute to the observed high levels of marital instability and high levels of short and long term migration in Kisesa, especially among younger adults. Marriage and migration patterns are important underlying factors affecting the spread of HIV. The most cost-effective intervention strategy may be to focus on the trading centre in which mobility is higher, bars were more common, and HIV prevalence and incidence were considerably higher than in the nearby rural villages. If resources suffice, additional work can be undertaken in the rural villages, although it is not clear to what extent the rural epidemic would be self sustaining if the interventions in the trading centre were effective.
Solitary cerebellous metastasis after prolonged remission in a case of uterine cervical adenocarcinoma

Intracranial metastasis of a uterine cervical carcinoma is a very rare occurrence. These metastases are characteristically multiple, supra-tentorial, associated with multiple systemic dissemination, usually occur relatively late in the course of the disease, and are most often seen in squamous carcinomas. We present an unusual case which defied these characteristics. This patient was in long-term remission (11 years), presented with a solitary cerebellous metastases, had no evidence of other systemic spread, and the pathology was an adenocarcinoma. We present this rare case with interesting clinical ramifications. This is probably the longest duration of remission prior to the metastasis in the published literature.
9. Mixing in Lakes and Reservoirs

Mixing in lakes and reservoirs is largely controlled by stratification. Stratification reduces vertical exchange and can drive horizontal exchange by enforcing a preferred vertical structure. Stratification arises from temperature, dissolved solids and suspended particulate variations. The latter two components (chemical and suspended particulate stratification) are generally negligible in the bulk fluid of inland lakes and reservoirs. Thus, stratification is dominantly dependent on temperature variation, which in turn is a function of the overall energy balance and the internal mixing processes of a lake. This chapter begins by discussing the development of stratification followed by a description of the energy inputs to a lake or reservoir. From the annual energy input variation a typical annual cycle for a temperate lake is introduced: lakes are stratified in winter and summer and have complete mixing events, called turnover, that occur in the spring and fall. The chapter closes with a brief introduction to the dominant mixing processes that influence the stratification structure. These mixing processes are also the dominant processes affecting the fate and transport of contaminants in lakes and reservoirs. Reservoir dynamics is an active and important area of research in environmental fluid mechanics. Many of the concepts introduced here are general. They relate to most lakes and help understand the important characteristics of stratification. The detailed mixing processes, however, can be significant and quite complicated. For instance, exchange between sediments and the open water can be controlled by sieches, groundwater exchange, redox chemistry, and microturbulence, among other factors. The interested reader is encouraged to get more details in Imboden & Wüest (1995), Lorke et al. (2003), and Fischer et al. (1979) and their bibliography sections.
L'annotation formelle de documents en (8) questions

Annoter un ensemble de documents informels a l'aide de representations formelles appelle plusieurs questions qui doivent trouver une reponse si l'on veut developper un systeme coherent. Ces questions sont liees a la forme et a l'objet des representations retenues, a la necessite d'utiliser de la connaissance independante du contenu des documents (ontologies, connaissance de contexte) et au statut du systeme resultant (grande base de connaissance ou elements de connaissance distribues). Ces questions sont decrites et illustrees par l'annotation de resumes d'articles en genetique moleculaire.
Agribusiness Perspectives – Paper 60 Managing Herbicide Resistance : The Role of Extension 1 Agribusiness Perspectives – Paper 60 Managing Herbicide Resistance : The Role of Extension

The rapid evolution of herbicide resistance poses a significant threat for conventional agricultural practices. In practice, herbicide resistance seems to be a very complicated problem to deal with. Extension can play a significant role in managing herbicide resistance educating farmers on the main advantages and disadvantages of the available methods aiming to control and minimize herbicide resistance. This could be achieved by redirecting the educational efforts more towards the principles of weed biology and integrated weed management, teaching farmers how to learn, paying attention to the basic prerequisites for the new control methods and providing precise information about the economic usefulness of each proposed method. Introduction The occurrence of herbicide-resistant weeds has become a common and almost worldwide phenomenon, particularly the last few years, due to the continuous use of herbicides as the main method of weed control, in combination with monoculture cropping systems (Shaner, 1995). Such cropping systems, developed since the discovery of selective herbicides, rely mainly on high efficacy and cost effectiveness of herbicides for maximum crop productivity and intensive use of land. However, the strong selection pressure imposed to weed populations by the continuous use of herbicides has resulted in development of resistance. Herbicide resistance poses a major threat to conventional agricultural practices as, to date, more than 250 weed biotypes in 50 countries have been reported to be resistant to one or more than one herbicide(s) (Heap, 2002). Herbicide resistance is expected to strongly affect weed management strategies in the future (Duke, 1997). How herbicide resistance will ultimately influence agriculture may depend on many factors and may vary considerably with crop and location. It is evident, however, that when resistance has been extensively developed, weed management with certain herbicides becomes inadequate and different herbicides or other methods of weed control should be adopted. This may have a great impact on the agriculture of an area (Peterson, 1999). Farmers, on the other hand, do not seem to rapidly adopt new weed management strategies to delay the development of resistance. On the contrary, they tend to continue with a successful herbicide program until it fails and only when resistance to herbicides fully occurs they adjust their weed management practices accordingly (Pannell and Zilberman, 2001). 1 Research Agronomist, Laboratory of Agronomy, Aristotle University of Thessaloniki 541 24, Thessaloniki, Greece damalas@weedmail.com
Exhibit G: Mitochondrial Dysfunction and Disruption of Electrophysiology

Mitochondria are broadly vulnerable, in part because the integrity of their membranes is vital to their optimal functioning – including channels and electrical gradients, and their membranes can be damaged by free radicals which can be generated in myriad ways. Moreover, just about every step in their metabolic pathways can be targeted by environmental agents, including toxicants and drugs, as well as mutations [1]. This supports a cumulative allostatic load model for conditions in which mitochondrial dysfunction is an issue, which includes autism as well as myriad other chronic conditions.