Miracle-dz/UniFAR-FTUs huggingface dataset:
A Review of Bioinformatics Education in the UK

If the completion of the first draft of the human genome represents the coming of age of bioinformatics, then the emergence of bioinformatics as a university degree subject represents its establishment. In this paper bioinformatics as a subject for formal study is discussed, rather than as a subject for research, and a selection of the taught, mainly graduate, courses currently available in the UK are reviewed. Throughout, the author tries to draw parallels between the integration of bioinformatics into biomedical research and teaching today, and that of molecular biology, two decades ago. Others have made this analogy between these two relatively young disciplines. Although research sources are referenced, the author makes no pretence of objectivity. This article contains his opinions, and those of a number of current bioinformatics course organisers whose comments on the subject were solicited in advance specifically for this paper. The course organisers kindly advised how they planned their curricula, and described the special strengths of their programmes. Comments from present and former students of several bioinformatics degree programmes were also solicited. Except where individuals are directly quoted, any opinions expressed herein should be considered the author's. Compared with its sister piece [Marion Zatz, in previous issue of Briefings in Bioinformatics pp. 353], this paper is less about funding policy--which, in the UK, has lately (if belatedly) been more generous towards bioinformatics teaching--than it is about practice and content; the requirements of the bioinformatics research communities, the corresponding emphases of bioinformatics courses, and the general market for holders of bioinformatics degrees. Individual courses are cited throughout as examples, but the final section contains a full annotated listing with URL addresses. Based on the author's own experience of practising and teaching bioinformatics, he describes the skills he believes will be most useful to bioinformaticians in the near future and suggests ways to prepare students of bioinformatics for a fall in demand for those abilities.
Strategy to decrease the risk of adverse effects of fragrance ingredients in cosmetic products.

In spite of extensive self-regulation of the fragrance industry, fragrance ingredients are still major causes of allergic contact dermatitis. There are indications that the problem is increasing in some countries, and that many nonregulated compounds are involved in the development of allergies. The use of essential oils in fragrance compounds might add both allergenic and carcinogenic compounds to a product and the exact composition of such ingredients is difficult to control. Herein, we propose a simple strategy to decrease the risk of adverse effects of fragrance ingredients in cosmetic products. This strategy consists of four major steps: (1) limit the concentration of fragrance compound in the products, (2) follow legislation and guidelines, (3) limit the concentration of a number of well-known sensitizing fragrance chemicals, and (4) limit the concentration of essential oils and materials with unknown composition. The strategy is discussed as an alternative to animal testing and in relation to other more resource-demanding approaches to the same problem.
Ultrafast Surface Imaging With an Increased Spatial Resolution Based on Polarization-Division Multiplexing

Optical time stretch has been employed for ultrafast optical imaging based on space-to-wavelength-to-time mapping. However, temporal overlap between two adjacent time-stretched pulses is a disadvantageous factor that limits the spatial resolution, or the frame rate has to be reduced by reducing the pulse repetition rate to avoid the temporal overlap. To increase the spatial resolution without reducing the frame rate, we propose a novel technique based on polarization-division multiplexing, using a polarization modulator to generate two polarization interleaved pulse trains. Since two adjacent optical pulses are orthogonally polarized, the spacing between two adjacent pulses for one polarization direction is doubled, and the spatial resolution is doubled by using a dispersive element with two times the dispersion. The proposed approach is experimentally evaluated. An imaging system with an increased spatial resolution is demonstrated.
The Distribution of Population and Employment in a Polycentric City: The Case of Los Angeles

The distribution of population and employment in metropolitan Los Angeles in 1970 and 1980 is examined in this paper. Population continued to disperse in the 1970s, whereas the geographical distribution of employment combined job clustering around a few major employment centers with a high degree of general job dispersion. In Los Angeles polycentrism has been associated with shorter work trips, particularly intracounty trips in the more peripheral counties.
A type of sensor to detect occupancy of vehicle berth in carpark

To provide accurate, real time car park space information, based on the vortex detection principle, a novel berth detector is designed for the parking guidance system. The berth-detecting algorithm is proposed according to the complicated practical car park situation via threshold method. The median filter technology is adopted in this algorithm to eliminate transient-upset signal. The experimental results show that the vortex berth detector has strong robustness under rapid time-varying temperature condition, and the algorithm is efficient and reliable.
The prevalence, cost and basis of food allergy across Europe

The development of effective management strategies to optimize the quality of life for allergic patients is currently hampered by a lack of good quality information. Estimates of how many individuals suffer from food allergy and the major foods involved vary widely and inadequacies of in vitro diagnostics make food challenges the only reliable means of diagnosis in many instances. The EuroPrevall project brings together a multidisciplinary partnership to address these issues. Cohorts spanning the main climatic regions of Europe are being developed in infants through a birth cohort, community surveys in school‐age children and adults and an outpatient clinic study. Confirmatory double‐blind placebo‐controlled food challenge diagnosis is being undertaken using foods as they are eaten with titrated doses to allow no‐effect and lowest‐observable effect levels for allergenic foods to be determined. The cohorts will also facilitate validation of novel in vitro diagnostics through the development of the EuroPrevall Serum Bank. Complementary studies in Ghana, western Siberia, India and China will allow us to gain insights into how different dietary patterns and exposure to microorganisms affect food allergies. New instruments to assess the socioeconomic impact of food allergy are being developed in the project and their application in the clinical cohorts will allow, for the first time, an assessment to be made of the burden this disease places on allergy sufferers and their communities.
Spatial Coordination of Cytokinetic Events by Compartmentalization of the Cell Cortex

During cytokinesis, furrow ingression and plasma membrane fission irreversibly separate daughter cells. How actomyosin ring assembly and contraction, vesicle fusion, and abscission are spatially coordinated was unknown. We found that during cytokinesis septin rings, located on both sides of the actomyosin ring, acted as barriers to compartmentalize the cortex around the cleavage site. Compartmentalization maintained diffusible cortical factors, such as the exocyst and the polarizome, to the site of cleavage. In turn, such factors were required for actomyosin ring function and membrane abscission. Thus, a specialized cortical compartment ensures the spatial coordination of cytokinetic events.
Automatic saboteur placement for emulation-based multi-bit fault injection

During recent years the dependability and security requirements of system-on-chip (SoC) designs have increased tremendously. Both, dependability and security, domains are concerned with operational faults of a random or intentional nature. In former case random faults e.g. caused by radiation or degradation effects could lead to execution errors with possible dramatic results. The security domain is more concerned with intentional faults injected by an adversary during a physical attack to drive the system into an unintended state. The resistance of such a design against faults can be emulated during early design phases using fault injection methods. For these methods the design-under-test is augmented with additional circuitry to emulate faults at predestined locations. One method uses saboteurs, elements that are transparent during normal operation and faulty if activated, are placed into the target system. If this placement process includes a high number of saboteurs, the hardware description manipulation could be a challenge for the design engineer. Therefore this paper presents an automatic placement methodology for fault injection evaluations using saboteur techniques. The automatized process allows for the efficient placement of large amounts of saboteurs. This enables the designer to evaluate a high number of different dependability and fault attack scenarios during early design phases using FPGA-based functional emulation. Selected case studies show how this approach can be applied to a common general purpose architecture in an efficient way.
Loneliness, depression, and social support of Turkish patients with chronic obstructive pulmonary disease and their spouses.

PURPOSE To identify the differences in loneliness, depression, and social support among Turkish patients with COPD and their spouses. DESIGN The convenience sample consisted of 30 patients with COPD and their spouses. Descriptive statistics, Student's t tests, and Pearson product moment correlations were used to analyse the data. METHODS Data were collected during structured interviews in an outpatient clinic in Turkey by using the UCLA Loneliness Scale, the Beck Depression Inventory and Perceived Social Support from Friends and Family scales. FINDINGS Levels of loneliness, depression, and perceived social support from family and friends were similar for patients and spouses. Loneliness and depression were positively related, but both loneliness and depression were greater with less perceived social support from family and friends for both patients and their spouses. CONCLUSIONS Patients' and spouses' psychologic reactions to COPD might include feelings of loneliness and depression, which might be alleviated by social support.
Phaeohyphomycosis Caused by the Fungal Genera Bipolaris and Exserohilum: A REPORT OF 9 CASES AND REVIEW OF THE LITERATURE

We have reported 7 new cases of Bipolaris infection and 2 of Exserohilum infection, which demonstrate the capability of these 2 genera to cause invasive as well as "allergic" disease. As noted previously, it is likely that all of the cases of "Helminthosporium" and Drechslera infections reported in the literature were caused by Bipolaris or Exserohilum. Infections due to these 2 genera are probably more common than previously recognized. They should be included in the differential diagnosis of central nervous system and disseminated fungal disease, sinusitis, keratitis, peritonitis associated with continuous ambulatory peritoneal dialysis, and allergic bronchopulmonary disease. These various entities have distinct histopathologic characteristics. With disseminated disease in the immunocompromised patient, the most frequent findings are acute inflammation with prominent vascular invasion, thrombosis, and infarction. In contrast, granulomatous inflammation and leukocytoclastic vasculitis are seen in meningoencephalitis caused by these fungi. The histologic features of allergic bronchopulmonary disease and sinusitis are similar. A chronic inflammatory infiltrate of lymphocytes, plasma cells and eosinophils within edematous granulation tissue is found in addition to squamous metaplasia and thickening of the basement membrane. Infections caused by Bipolaris/Exserohilum and Aspergillus show many clinical and pathologic similarities despite the lack of taxonomic relationship between these fungi. Both cause disseminated disease in immunocompromised patients that is characterized by tissue necrosis and vascular invasion. Both cause central nervous system disease, osteomyelitis, and sinusitis and are associated with allergic bronchopulmonary disease. Sinusitis, the most common form of disease caused by Bipolaris and Exserohilum, occurs in otherwise healthy patients with nasal polyposis and allergic rhinitis. Although pathologic evidence of bone invasion may not be found, there frequently is radiographic evidence of invasive disease. Most patients who are treated initially with surgical debridement and amphotericin B have apparently been cured. However, longer follow-up will be necessary in these patients. Amphotericin B appears to be the treatment of choice for invasive infections caused by Bipolaris/Exserohilum species. Ketoconazole and other imidazole derivatives may also be effective in certain of the disease entities caused by these black moulds; however, their role has yet to be defined. (ABSTRACT TRUNCATED AT 400 WORDS)
Failure modes of planar and trench SiC MOSFETs under single and multiple short circuits conditions

An analysis of the failure modes due to short circuit on planar and trench 1200ν — 40mΩ SiC-MOSFETs is presented, including single and multiple events. Short circuit waveforms, energy, as well as electro-thermal simulations are presented, enabling the identification of the main root causes of failure. Results demonstrate similar performance regarding failure after turn-off (thermal runaway, gate) for both technologies, nevertheless the SiC-MOSFET trench variant showed superior response after multiple faults.
Monnaie, prix, change et développement : le cas des économies exportatrices de pétrole du Tiers-Monde

Cet article a pour objectif l'etude de la monnaie, des prix et du taux de change dans une economie exportatrice d'hydrocarbures. Le role determinant de la rente petroliere dans ce type d'economie lui confere des caracteristiques macroeconomiques specifiques tres differentes de celles qui caracterisent une economie de production. L'analyse comparee des economies petrolieres du tiers-monde et de la Grande-Bretagne met en evidence l'impact discriminatoire exerce par la rente sur le prix des biens commerciaux et non commerciaux via la reappreciation "naturelle" du taux de change. Le secteur productif est decourage au profit du secteur des biens non commerciaux (bien souvent speculatifs). Cet effet - observable partout - ajourne et peut-etre compromet pour longtemps l'avenement de "l'apres petrole". Les pays petroliers ne peuvent donc eluder le role joue par les variables financieres et monetaires - notamment la politique du taux de change - dans la mise en place du processus de developpement (Resume d'auteur)
Context effects and inefficient initiation at non-AUG codons in eucaryotic cell-free translation systems

The context requirements for recognition of an initiator codon were evaluated in vitro by monitoring the relative use of two AUG codons that were strategically positioned to produce long (pre-chloramphenicol acetyl transferase [CAT]) and short versions of CAT protein. The yield of pre-CAT initiated from the 5'-proximal AUG codon increased, and synthesis of CAT from the second AUG codon decreased, as sequences flanking the first AUG codon increasingly resembled the eucaryotic consensus sequence. Thus, under prescribed conditions, the fidelity of initiation in extracts from animal as well as plant cells closely mimics what has been observed in vivo. Unexpectedly, recognition of an AUG codon in a suboptimal context was higher when the adjacent downstream sequence was capable of assuming a hairpin structure than when the downstream region was unstructured. This finding adds a new, positive dimension to regulation by mRNA secondary structure, which has been recognized previously as a negative regulator of initiation. Translation of pre-CAT from an AUG codon in a weak context was not preferentially inhibited under conditions of mRNA competition. That result is consistent with the scanning model, which predicts that recognition of the AUG codon is a late event that occurs after the competition-sensitive binding of a 40S ribosome-factor complex to the 5' end of mRNA. Initiation at non-AUG codons was evaluated in vitro and in vivo by introducing appropriate mutations in the CAT and preproinsulin genes. GUG was the most efficient of the six alternative initiator codons tested, but GUG in the optimal context for initiation functioned only 3 to 5% as efficiently as AUG. Initiation at non-AUG codons was artifactually enhanced in vitro at supraoptimal concentrations of magnesium.
HYPOTHETICAL I NTERTEMPORAL C ONSUMPTION CHOICES

The paper extends and replicates part of the analysis by Barsky et al. (1997), which exploits hypothetical choices among different consumption streams to infer intertemporal substitution elasticities and rates of time preference. We use a new and much larger dataset than Barsky et al. Furthermore, we estimate structural models of intertemporal choice, while parameterising the parameters of interest as a function of relevant individual characteristics. We also consider ‘behavioural’ extensions, like habit formation. Models with habit formation appear to be superior to models with intertemporally additive preferences. Time preference has been extensively measured through survey techniques. In general, respondents face a hypothetical situation involving different amounts of money (or some other desirable good) at different points in time and are asked to either express a preference for one of the alternatives or to provide a trade-off (how much money does one require to postpone the receipt of a certain amount for instance). Discount rates measured in this way were found to be negatively correlated with future time orientation and positively correlated with big spending (Thomas and Ward, 1979). Kurz et al. (1973) asked a sample of participants in the Seattle and Denver Income Maintenance Experiments a series of hypothetical questions such as: ‘What size bonus would you demand today rather than collect a bonus of $100 in 1 year? ’. They found a mean rate of time preference between 0.36 and 0.76, and between 0.40 and 1.22 for whites and for blacks, respectively. Although these rates of time preference may seem implausibly high, high rates are also found in revealed preference studies. In a well-known study, Hausman (1979) used individual household data on the purchase and utilisation of room air conditioners to estimate the intertemporal discount rates used by consumers in order to evaluate the trade-off between present and future costs. He found an estimated average annual discount rate of 26.4% (clearly above any relevant interest rate) and an inverse relation with income. Loewenstein and Thaler (1989) cite a number of other studies that find even larger discount rates. Explanations that have been offered include information barriers and liquidity constraints. Further explanations have been provided by Kooreman (1995), whose main conclusion is that if risk-neutral consumers anticipate a random lifetime of a durable, the assumption of a deterministic lifetime results in an upward bias, as large as 35%, of estimated discount rates.
Oligonucleotide Fingerprinting of rRNA Genes for Analysis of Fungal Community Composition

ABSTRACT Thorough assessments of fungal diversity are currently hindered by technological limitations. Here we describe a new method for identifying fungi, oligonucleotide fingerprinting of rRNA genes (OFRG). ORFG sorts arrayed rRNA gene (ribosomal DNA [rDNA]) clones into taxonomic clusters through a series of hybridization experiments, each using a single oligonucleotide probe. A simulated annealing algorithm was used to design an OFRG probe set for fungal rDNA. Analysis of 1,536 fungal rDNA clones derived from soil generated 455 clusters. A pairwise sequence analysis showed that clones with average sequence identities of 99.2% were grouped into the same cluster. To examine the accuracy of the taxonomic identities produced by this OFRG experiment, we determined the nucleotide sequences for 117 clones distributed throughout the tree. For all but two of these clones, the taxonomic identities generated by this OFRG experiment were consistent with those generated by a nucleotide sequence analysis. Eighty-eight percent of the clones were affiliated with Ascomycota, while 12% belonged to Basidiomycota. A large fraction of the clones were affiliated with the genera Fusarium (404 clones) and Raciborskiomyces (176 clones). Smaller assemblages of clones had high sequence identities to the Alternaria, Ascobolus, Chaetomium, Cryptococcus, and Rhizoctonia clades.
Methods for observing microbial biofilms directly on leaf surfaces and recovering them for isolation of culturable microorganisms

Epifluorescence microscopy, scanning electron microscopy, and confocal laser scanning microscopy were used to observe microbial biofilms directly on leaf surfaces. Biofilms were observed on leaves of all species sampled (spinach, lettuce, Chinese cabbage, celery, leeks, basil, parsley, and broad-leaved endive), although the epifluorescent images were clearest when pale green tissue or cuticle pieces were used. With these techniques, biofilms were observed that were about 20 (mu)m in depth and up to 1 mm in length and that contained copious exopolymeric matrices, diverse morphotypes of microorganisms, and debris. The epifluorescence techniques described here can be used to rapidly determine the abundance and localization of biofilms on leaves. An additional technique was developed to recover individual biofilms or portions of single biofilms from leaves and to disintegrate them for isolation of the culturable microorganisms they contained. Nineteen biofilms from broad-leaved endive, spinach, parsley, and olive leaves were thus isolated and characterized to illustrate the applications of this technique.
Endogenous glucocorticoids decrease skeletal angiogenesis, vascularity, hydration, and strength in aged mice

Aging or glucocorticoid excess decrease bone strength more than bone mass in humans and mice, but an explanation for this mismatch remains elusive. We report that aging in C57BL/6 mice was associated with an increase in adrenal production of glucocorticoids as well as bone expression of 11β‐hydroxysteroid dehydrogenase (11β‐HSD) type 1, the enzyme that activates glucocorticoids. Aging also decreased the volume of the bone vasculature and solute transport from the peripheral circulation to the lacunar‐canalicular system. The same changes were reproduced by pharmacologic hyperglucocorticoidism. Furthermore, mice in which osteoblasts and osteocytes were shielded from glucocorticoids via cell‐specific transgenic expression of 11β‐HSD type 2, the enzyme that inactivates glucocorticoids, were protected from the adverse effects of aging on osteoblast and osteocyte apoptosis, bone formation rate and microarchitecture, crystallinity, vasculature volume, interstitial fluid, and strength. In addition, glucocorticoids suppressed angiogenesis in fetal metatarsals and hypoxia inducible factor‐1α transcription and vascular endothelial growth factor production in osteoblasts and osteocytes. These results, together with the evidence that dehydration of bone decreases strength, reveal that endogenous glucocorticoids increase skeletal fragility in old age as a result of cell autonomous effects on osteoblasts and osteocytes leading to interconnected decrements in bone angiogenesis, vasculature volume, and osteocyte‐lacunar‐canalicular fluid.