Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction and Explanation by Combined Model-Based and Case-Based Reasoning

Case-based reasoning is suitable for capturing and reusing human experiences for complex problem solving, and has earlier shown its success also in the oil drilling domain[1]. However, a pure CBR system suffers from the inability to justify a solution beyond referring to the best matching case or cases. Further, CBR represents in itself a knowledge-lean method for case retrieval. A model of general domain knowledge would enable cases to be matched based on semantic rather than purely syntactic criteria. Hence, a general domain model combined with CBR will enable the system to generate targeted explanations for the user as well as for its internal reasoning process. Earlier work in our group have addressed this problem by combining CBR with a semantic network of multi relational domain knowledge [2], which implementation is called TrollCreek. A problem with that method was the lack of a formal basis for the semantic network that was used, which made the inference processes within the network difficult to develop and less powerful than wanted. The need for a more formal treatment of uncertainty leads to some initial investigations into how a Bayesian Network (BN) model could be incorporated [3, 4]. Bayesian Network has shown its feasibility to build probabilistic models without introducing unrealistic assumptions of independencies [4]. The probability distribution provided by BN enables the conditioning over any of the variables and supports any direction of reasoning [5]. Also, the Bayesian Networks framework includes an inference engine, which, given some evidence, is capable of updating its beliefs [6]. Moreover, the nature of Bayesian Networks allows for some explanations to be given regarding the reasoning process [4]. All these make BNs a proper candidate for my PhD work.
Coordinate Regulation of Lipid Metabolism by Novel Nuclear Receptor Partnerships

Mammalian nuclear receptors broadly influence metabolic fitness and serve as popular targets for developing drugs to treat cardiovascular disease, obesity, and diabetes. However, the molecular mechanisms and regulatory pathways that govern lipid metabolism remain poorly understood. We previously found that the Caenorhabditis elegans nuclear hormone receptor NHR-49 regulates multiple genes in the fatty acid beta-oxidation and desaturation pathways. Here, we identify additional NHR-49 targets that include sphingolipid processing and lipid remodeling genes. We show that NHR-49 regulates distinct subsets of its target genes by partnering with at least two other distinct nuclear receptors. Gene expression profiles suggest that NHR-49 partners with NHR-66 to regulate sphingolipid and lipid remodeling genes and with NHR-80 to regulate genes involved in fatty acid desaturation. In addition, although we did not detect a direct physical interaction between NHR-49 and NHR-13, we demonstrate that NHR-13 also regulates genes involved in the desaturase pathway. Consistent with this, gene knockouts of these receptors display a host of phenotypes that reflect their gene expression profile. Our data suggest that NHR-80 and NHR-13's modulation of NHR-49 regulated fatty acid desaturase genes contribute to the shortened lifespan phenotype of nhr-49 deletion mutant animals. In addition, we observed that nhr-49 animals had significantly altered mitochondrial morphology and function, and that distinct aspects of this phenotype can be ascribed to defects in NHR-66– and NHR-80–mediated activities. Identification of NHR-49's binding partners facilitates a fine-scale dissection of its myriad regulatory roles in C. elegans. Our findings also provide further insights into the functions of the mammalian lipid-sensing nuclear receptors HNF4α and PPARα.
Sagittal spine movements of small therian mammals during asymmetrical gaits

SUMMARY Mammalian locomotion is characterized by the use of asymmetrical gaits associated with extensive flexions and extensions of the body axis. Although the impact of sagittal spine movements on locomotion is well known, little information is available on the kinematics of spinal motion. Intervertebral joint movements were studied in two metatherian and three eutherian species during the gallop and halfbound using high-speed cineradiography. Fast-Fourier transformation was used to filter out high frequency digitizing errors and keep the lower frequency sinusoid oscillations that characterize the intervertebral angular movements. Independent of their regional classification as thoracic or lumbar vertebrae, 7±1 presacral intervertebral joints were involved in sagittal bending movements. In only one species, no more than five intervertebral joints contributed to the resulting `pelvic movement'. In general, the trunk region involved in sagittal bending during locomotion did not correspond to the traditional subdivisions of the vertebral column (e.g. as thoracic and lumbar or pre- and postdiaphragmatic region). Therefore, these classifications do not predict the regions involved in spinal oscillations during locomotion. Independent of the gait, maximum flexion of the spine was observed in the interval between the last third of the swing phase and touch-down. This results in a retraction of the pelvis and hindlimbs before touch-down and, we hypothesize, enhances the stability of the system. Maximum extension occurred during the first third of the swing phase (i.e. after lift-off) in all species. In general, the observed timing of dorsoventral oscillations of the spine are in accordance with that observed in other mammals and with activity data of respiratory and epaxial back muscles. Although no strict craniocaudal pattern was observable, the more cranial intervertebral joints tend to flex and extend earlier than the more caudal ones. This is in accordance with the organization and the activation of the paravertebral musculature in mammals. The amplitude of intervertebral joint movements increased caudally, reaching its highest values in the presacral joint. The more intense sagittal bending movements in the caudal intervertebral joints are reflected by the muscle fiber type composition of the back muscles involved. Despite the highly similar amplitude of `pelvic motion', touch-down and lift-off positions of the pelvis were clearly different between the species with a long, external tail and those with no external tail.
The Association Between Chronic Back Pain and Psychiatric Disorders; Results from a Longitudinal Population-Based Study

Chronic back pain is a common pain condition; it results in significant personal, social and occupational impairment, role disability and health care utilization.30, 34, 9, 32, 24 Epidemiologic studies have found that chronic back pain is comorbid with psychiatric disorders, other chronic pain conditions (migraine, arthritis, headache) and chronic psychical conditions.26, 15, 30, 5, 13 Most of the published studies regarding the assocation between chronic back pain and psychiatric disorders focus on the association with major depression.30, 5, 21, 22, 4 It is found that the prevalence of major depression among persons with chronic pain is about 2-3 times higher than among pain-free individuals.18 A study conducted by Von Korff et al. (2005) showed that chronic back pain is also significantly associated with mood, anxiety (except agoraphobia without panic) and alcohol abuse and dependence disorders.30 A recent international study conducted by Tsang et al. (2008) found that various chronic pain conditions (headache, back or neck pain, arthritis or joint pain) are associated with depression-anxiety spectrum disorders both in developed and developing countries.29 Although an association between chronic back pain and psychiatric disorders has been repeatedly demonstrated, little is known about the temporal relationship between the two, as most studies are based on clinical samples and cross-sectional data.6 Fishbain et al. (1997) analysed 40 studies addressing the temporal relationship between generic pain and major depression. However, no firm conclusions could be drawn as most of these studies differed in study design, methods and definition to identify depression.11 Fishbain et al. (1997) stated that more support was found for the hypothesis that pain precedes depression, although some of the selected studies found depression to be a predictor of first onset pain.22, 31, 4, 16, 3, 20 The aims of the present study are: 1. To assess cross-sectionally the association between chronic back pain and various mood, anxiety and substance use disorders; 2. To assess longitudinally the temporal relationship between chronic back pain and psychiatric disorders.
Nanoscale Characterization of Failure Processes in Polymer Nanocomposites

Abstract : This project was focused on two areas of investigation: application of novel displacement modulation techniques for nanoindentation based viscoelastic characterization; and the use of acoustic emission characterize nanoindentation induced fracture in brittle materials and advanced. A new displacement modulation technique has been developed and employed for determining the storage and loss moduli of viscoelastic polymers, as a function of frequency. This new technique represents a highly superior approach in comparison will all other existing techniques for dynamic indentation. Acoustic emission sensing has been established as a robust technique for quantifying failure in brittle materials, advanced ceramics and a new type of amorphous ceramic material. Collaboration with various researchers at the US Army Research Laboratory at Aberdeen Proving Ground provided fruitful benefits.
All-Optical Logic Gate for XOR Operation Between 40-Gbaud QPSK Tributaries in an Ultra-Short Silicon Nanowire

We demonstrate an all-optical XOR logic gate for 40-Gbaud quadrature phase-shift keying (QPSK) tributaries in a silicon nanowire for the first time. The XOR logic operation is realized based on four-wave mixing (FWM) in the C-band. Experimental results show negligible power penalty at a bit error ratio (BER) of 10-6 compared with the back-to-back signals. The BER floor appears at BER of 10-6 for both I and Q tributaries of the logic operation, and the main reasons are the optical signal-to-noise ratio (OSNR) deterioration caused by nonlinear loss due to free carrier absorption (FCA) and two-photon absorption (TPA) and the cross-phase modulation (XPM)-induced phase impairments.
Additional Records of Freshwater Shrimp (Malacostraca: Crustacea) from Greater Zab River and Their Banks, Iraq

Physicochemical and biological samples in two artificial sand mine ponds and Greater Zab River were collected during July to December 2015, in order to evaluate water quality of these studied ecosystems and their effect on existing of two freshwater shrimps, Mysis relicta which was recorded and described as a new record for Iraqi fauna while Macrobrachium nipponense was recorded in southern part of Iraq before more than decades but it regarded as new record in the northern part of Iraq (Kurdistan region). Results showed that pH values were in alkaline side of neutrality, EC in pond 1 was higher than other two sites, dissolved oxygen did not fall under 5 mg.l -1 and BOD 5 values were high and not suitable for drinking purpose. Sources of nutrient in the studied sites comes from runoff and domestic discharge. Mysis relicta characterized by living in cooled, well aerated ecosystem, but in the present study we found it in ponds with water temperature over 20 °C and oxygen content less than 9 5 mg.l -1 .
Determinants of Food Security in Kenya, a Gender Perspective

The paper contributes to an understanding of the determinants of food security with a bias on the link between gender of household head and food security using detailed farm household and plot level survey data from 30 divisions in rural Kenya. Both parametric and non-parametric econometric techniques are used to ensure robustness of the results from the econometric analyses. Since the assumption of pooled regression is rejected, we run separate food security regressions at plot level both for Male Headed Households (MHHs) and Female Headed Households (FHHs). Both descriptive and econometrics results shows that FHHs in general are more likely to be food insecure compared to their male counterparts. The analysis further reveals that Female Headed Households‘ food security increases with quality of extension workers; land quality, farm size while distance to the market reduces the probability of food security. For the quality of extension staff, policy makers should focus on improving the skill of extension staff for efficient and effective dissemination of technologies and other important information that has impact on food security. Since area expansion is infeasible due to land scarcity in Kenya, policy makers focusing on land augmenting practices can help farm households to escape food insecurity.
The assessment of surface areas in porous carbons by two model-independent techniques , the DR equation and DFT

The strong linear correlation observed between SBET and the micropore volume of 190 carbons with pore widths between 0.5 and 1.8 nm confirms the unreliable character of SBET, in spite of its frequent use. (It corresponds approximately to 2200-2300 m per cm of micropores, whatever their width). Alternative determinations of the surface area are therefore required. It is shown that two model-independent techniques (Kaneko’s comparison plot for nitrogen and the enthalpies of immersion into aqueous solutions of phenol) and two model-dependent approaches (Dubinin’s theory and DFT) lead to total surface areas which are in good agreement. Their average Sav is probably a reliable assessment of the total surface area. It is often in disagreement with SBET, but a closer study of 42 well characterized microporous carbons, for which all four techniques are available, shows that the ratio SBET/Sav increases linearly with the average pore width. This should be taken into consideration when surface-related properties (e.g. densities of chemical groups or adsorbed species, specific capacitances) are examined on the basis of a single determination and in particular on the BET technique. ______________________________________________________________________ *Corresponding author: Fax: +41 32 7182511. E-mail address: fritz.stoeckli@unine.ch
Immunopathological and Molecular Approaches for the Diagnosis of Salmonellosis in Natural Cases of Bovine Abortion

Rapid and precise diagnosis in natural field cases of bovine abortion warrants use of most sensitive and reliable diagnostic methods. In the present study, histopathological, immuno-histochemical and PCR technique(s) have been applied for diagnosis of abortion cases due to Salmonellosis. Histopathologically, multifocal lymphoid granulomas were observed in liver of aborted fetuse(s) which showed positive immuno-reactivity to the anti-Salmonella polyclonal antibody. PCR for diagnosis of salmonellosis in the aborted bovine fetuses found two positive samples out of the total 113 samples tested. Primers S18/ S19 pair amplified a 159 bp region of the sequence encoding an ompC gene of Salmonella species.
Electronic Nose Technology for Detection of Invasive Pulmonary Aspergillosis in Prolonged Chemotherapy-Induced Neutropenia: a Proof-of-Principle Study

ABSTRACT Although the high mortality rate of pulmonary invasive aspergillosis (IA) in patients with prolonged chemotherapy-induced neutropenia (PCIN) can be reduced by timely diagnosis, a diagnostic test that reliably detects IA at an early stage is lacking. We hypothesized that an electronic nose (eNose) could fulfill this need. An eNose can discriminate various lung diseases through the analysis of exhaled volatile organic compounds (VOCs). An eNose is cheap and noninvasive and yields results within minutes. In a single-center prospective cohort study, we included patients who were treated with chemotherapy expected to result in PCIN. Based on standardized indications, a full diagnostic workup was performed to confirm invasive aspergillosis or to rule it out. Patients with no aspergillosis were considered controls, and patients with probable or proven aspergillosis were considered index cases. Exhaled breath was examined with a Cyranose 320 (Smith Detections, Pasadena, CA). The resulting data were analyzed using principal component reduction. The primary endpoint was cross-validated diagnostic accuracy, defined as the percentage of patients correctly classified using the leave-one-out method. Accuracy was validated by 100,000 random classifications. We included 46 subjects who underwent 16 diagnostic workups, resulting in 6 cases and 5 controls. The cross-validated accuracy of the eNose in diagnosing IA was 90.9% (P = 0.022; sensitivity, 100%; specificity, 83.3%). Receiver operating characteristic analysis showed an area under the curve of 0.93. These preliminary data indicate that PCIN patients with IA have a distinct exhaled VOC profile that can be detected with eNose technology. The diagnostic accuracy of the eNose for invasive aspergillosis warrants validation.
Isolation, Antibiogram and PCR Detection of Avibacterium paragallinarum from Poultry Flocks of India

Infectious coryza (IC), caused by Avibacterium paragallinarum, is one of the major problem affecting the commercial poultry industry worldwide including India. Very few reports regarding the prevalence of Av. paragallinarum in particular with the application of rapid, sensitive and confirmatory detection by the molecular tools are available from India. In this study a total of 105 field samples collected as nasal and sinus swabs from suspected cases of IC from different geographical locations viz. Bareilly (U.P), Pune (Maharashtra), Bangalore (Karnataka), Indore and Jabalpur (Madhya Pradesh) of India were analyzed. Cultural isolation revealed the presence of four different, NAD-dependent types of Av. paragallinarum positive isolates showing typical ‘satellite’ growth. Biochemically, all the isolates of Av. paragallinarum showed negative catalase activity, reduced nitrate to nitrite and unable to produce indole, hydrolysed the urea and fermented glucose and fructose without formation of gas and variability in acid production was observed with mannitol, mannose, and sorbitol. Antibiogram indicated that all field isolates were sensitive to Amoxycillin / Clavulanic acid, Enroflaxacin, Ciprofloxacin, Pefloxacin, Co-Trimoxazole and Chloramphenicol antibiotics. Furthermore, isolates were relatively less sensitive to Neomycin, Cephalaxin, Streptomycin and Furozolidin and resistant to Colistin, Ampicillin, Tetracycline, Oxytetracycline and Doxycycline antibiotics. PCR assay was standardized for direct detection of the causative bacterium on nasal and sinus swabs, culturally isolated colonies of Av. paragallinarum and reference strains by using combination of N1/R1 primers (HPG-2 gene based PCR) for evaluating the detection applicability of molecular diagnostic methodology. In conclusion, Av. paragallinarum was culturally isolated and biochemically characterized from field cases suspected of infectious coryza in poultry and presence of the causative bacterium was also confirmed by the molecular tool of PCR. Comparatively, PCR was found to be more effective and a sensitive diagnostic tool for rapid and reliable diagnosis of IC. Further, large scale epidemiological studies along with application of diagnostic molecular tools are suggested to know the real magnitude of this important pathogen affecting poultry flocks of the country.
Biosynthesis, Characterization and Biological Activates of Silver Nanoparticles by Streptomyces bikiniensis Strain Ess_amA-1

In the current study, Streptomyces bikiniensis was isolated from insect ( Tapinoma simrothi ), Riyadh, Saudi Arabia, and identified by classical and molecular methods. The biosynthesized silver nanoparticles (AgNPs) were characterized by determining Fourier transform infrared spectroscopy (FTIR), Energy Dispersive Spectroscopy (EDS) and transmission electron microscopy (TEM). TEM photos of nanoparticles showed the spherical shapes of nanoparticles in the size range of 3–70 nm. Moreover, the minimum inhibitory concentration of biosynthesized silver nanoparticles against Staphylococcus aureus , Streptococcus pyogenes , Klebsiella pneumonia, Pseudomonas aeruginosa and Salmonella typhi were at 8 µg per paper disc (6 mm), and the inhibition zones were 7 to 9 mm while was at 16µg per paper disc in case of Candida albicans , the inhibition zone was 8 mm. The lethal inhibitory concentration (IC 50 ) of AgNPs on Hep2 and MCF-7 cells was obtained at 253.6 and 119.6 µg/ml, respectively. Thus, bioconversion of silver nanoparticles by Streptomyces bikiniensis strain Ess_amA-1 can be employed as a potential Nano-drug to kill pathogenic microbes.
The Virtual Brain: a simulator of primate brain network dynamics

We present The Virtual Brain (TVB), a neuroinformatics platform for full brain network simulations using biologically realistic connectivity. This simulation environment enables the model-based inference of neurophysiological mechanisms across different brain scales that underlie the generation of macroscopic neuroimaging signals including functional MRI (fMRI), EEG and MEG. Researchers from different backgrounds can benefit from an integrative software platform including a supporting framework for data management (generation, organization, storage, integration and sharing) and a simulation core written in Python. TVB allows the reproduction and evaluation of personalized configurations of the brain by using individual subject data. This personalization facilitates an exploration of the consequences of pathological changes in the system, permitting to investigate potential ways to counteract such unfavorable processes. The architecture of TVB supports interaction with MATLAB packages, for example, the well known Brain Connectivity Toolbox. TVB can be used in a client-server configuration, such that it can be remotely accessed through the Internet thanks to its web-based HTML5, JS, and WebGL graphical user interface. TVB is also accessible as a standalone cross-platform Python library and application, and users can interact with the scientific core through the scripting interface IDLE, enabling easy modeling, development and debugging of the scientific kernel. This second interface makes TVB extensible by combining it with other libraries and modules developed by the Python scientific community. In this article, we describe the theoretical background and foundations that led to the development of TVB, the architecture and features of its major software components as well as potential neuroscience applications.
Incidence and occurrence time of clinical mastitis in Holstein cows

The aim of this study was to assess the incidence of clinical mastitis (CM) and its risk factors in 1725 Holstein cows. Data were collected from a private farm from 2008 to 2012. The analysis of risk factors, performed with logistic regression, showed that cows at parity 2, 3, and 4 had 65%, 88%, and 115% risk of mastitis, respectively. This risk was higher (P < 0.001) than in cows at first parity. Cows that calved from October to January had the highest (P < 0.05) risk of mastitis. The number of mastitis cases in cows at lactation 2, 3, and 4 was 18.5%, 25.9%, and 40.7%, respectively, and was higher compared to cows at first lactation. Furthermore, cows that calved from July to September showed the highest number of mastitis cases. Gamma regression parameter estimates showed that the onset time of mastitis 1 and 2 in cows that calved from October to January occurred at 16.3 and 8.5 days, respectively. This was later than cows calving from July to September. The study concluded that it is necessary to examine cows for CM during the first 2 months of lactation in order to prevent mastitis and decrease its rate of incidence.