Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a triacylglycerol lipase gene family in Candida deformans: molecular cloning and functional expression

The yeast Candida deformans CBS 2071 produces an extracellular lipase which was shown to catalyse the production of various esters by the esterification of free fatty acids, even in the presence of a large molar excess of water. To clone the gene encoding this extracellular lipase, Saccharomyces cerevisiae was transformed with C. deformans genomic libraries and screened for lipolytic activity on a medium containing rapeseed oil emulsion and rhodamine B. Three members of a lipase gene family (CdLIP1, CdLIP2 and CdLIP3) were cloned and characterized. Each deduced lipase sequence has a Gly–His–Ser–Leu–Gly–(Gly/Ala)–Ala conserved motif, eight cysteine residues and encodes an N‐terminal signal sequence. MALDI–TOF mass spectrometry analysis of a proteolytic digest of the lipase produced was used to obtain experimental evidence that the CdLIP1 gene encoded the extracellular lipase. Recombinant expression studies confirmed that the cloned genes encoded functional lipases. The three lipases are very similar to lipases from the related species Yarrowia lipolytica. Significant homologies were also found with several yeast and fungal lipases. As C. deformans CBS 2071 was previously considered to be synonymous with Y. lipolytica, the strains were compared for the extent of nucleotide divergence in the variable regions (D1/D2) at the 5′‐end of the large‐subunit (26S) ribosomal DNA (rDNA) gene. This rDNA region has diverged sufficiently to suggest that C. deformans is a separate species. The nucleotide sequences of the CdLIP1, CdLIP2 and CdLIP3 genes will appear in the EMBL nucleotide sequence database under Accession Nos AJ428393, AJ428394 and AJ428395, respectively. Copyright © 2003 John Wiley & Sons, Ltd.
Genitourinary Involvement in Human Brucellosis: A Retrospective Analysis of Thirty Two Cases

Introduction: Brucellosis is zoonotic infection caused by Brucella bacteria. It is endemic in Turkey. Brucellosis can be followed by genitourinary complications in 2-20% of cases. The most common genitourinary complication in males is unilateral brucellar epididymo-orchitis (BEO). However, it can also rarely cause acute interstitial nephritis, pyelonephritis, prostatitis, focal and diffuse glomerulonephritis and renal abscess. The purpose of this study was to evaluate patients with genitourinary involvement brucellosis. Materials and Methods: Thirty-two patients diagnosed with brucellosis and with a history of pain or swelling in the testes, scrotal redness, and sensitivity during urination or renal complaints were evaluated retrospectively. Results: Mean age of patients was 41.71±14.56 years. The most common symptoms were lethargy, high fever, sweating, lack of appetite, scrotal swelling and scrotal redness. Left testicular swelling was present in 13 cases, right testicular swelling in nine and bilateral involvement in three. The most common laboratory findings were leukocytosis, and C-reactive protein (CRP), sedimentation (ESR), aspartate aminotransferase (AST) and alanine aminotransferase (ALT) elevation. All cases were successfully resolved with medical treatment. Conclusion: Brucellosis must not be forgotten in genitourinary involvements, especially in endemic regions. Occupation, contact with animals and consumption of unpasteurized milk or milk products should be investigated at anamnesis. Antibiotic combinations are generally sufficient in treatment. Orchiectomy and other surgical procedures are rarely required.
Neutral oxygen spectral line formation revisited with new collisional data: large departures from LTE at low metallicity

Aims. A detailed study is presented, including estimates of the impact on elemental abundance analysis, of the non-local thermodynamic equilibrium (non-LTE) formation of the high-excitation neutral oxygen 777 nm triplet in model atmospheres representative of stars with spectral types F to K. Methods. We have applied the statistical equilibrium code MULTI to a number of plane-parallel MARCS atmospheric models covering late-type stars (4500 ≤ Teff ≤ 6500 K, 2 ≤ log g ≤ 5[ cgs], and−3.5 ≤ [Fe/H] ≤ 0). The atomic model employed includes, in particular, recent quantum-mechanical electron collision data. Results. We confirm that the O i triplet lines form under non-LTE conditions in late-type stars, suffering negative abundance corrections with respect to LTE. At solar metallicity, the non-LTE effect, mainly attributed in previous studies to photon losses in the triplet itself, is also driven by an additional significant contribution from line opacity. At low metallicity, the very pronounced departures from LTE are due to overpopulation of the lower level (3s 5 S o ) of the transition. Large line opacity stems from triplet-quintet intersystem electron collisions, a form of coupling previously not considered or seriously underestimated. The non-LTE effects generally become severe for models (both giants and dwarfs) with higher Teff. Interestingly, in metal-poor turn-off stars, the negative non-LTE abundance corrections tend to rapidly become more severe towards lower metallicity. When neglecting H collisions, they amount to as much as
Voicepedia: towards speech-based access to unstructured information

Currently there are no dialog systems that enable purely voice-based access to the unstructured information on websites such as Wikipedia. Such systems could be revolutionary for non-literate users in the developing world. To investigate interface issues in such a system, we developed VoicePedia, a telephone-based dialog system for searching and browsing Wikipedia. In this paper, we present the system, as well as a user study comparing the use of VoicePedia to SmartPedia, a Smartphone GUI-based alternative. Keyword entry through the voice interface was significantly faster, while search result navigation, and page browsing were significantly slower. Although users preferred the GUI-based interface, task success rates between both systems were comparable – a promising result for regions where Smartphones and data plans are not viable. Index Terms: dialog system, information access
Stable tracking in variable time-delay teleoperation

Describes an improved architecture, for the control of force-feedback teleoperation in the presence of variable communication time-delay between the master and the slave. It is based on wave variable transformations and identification of time delay properties. This scheme achieves better position and force tracking than similar architectures, by estimating the current value of time delay and compensating its variations by adjusting a single control parameter. We derive some of the analytical properties of this scheme, and we show system performance by simulating a simple Internet-based teleoperation system.
Data-Driven Answer Selection in Community QA Systems

Finding similar questions from historical archives has been applied to question answering, with well theoretical underpinnings and great practical success. Nevertheless, each question in the returned candidate pool often associates with multiple answers, and hence users have to painstakingly browse a lot before finding the correct one. To alleviate such problem, we present a novel scheme to rank answer candidates via pairwise comparisons. In particular, it consists of one offline learning component and one online search component. In the offline learning component, we first automatically establish the positive, negative, and neutral training samples in terms of preference pairs guided by our data-driven observations. We then present a novel model to jointly incorporate these three types of training samples. The closed-form solution of this model is derived. In the online search component, we first collect a pool of answer candidates for the given question via finding its similar questions. We then sort the answer candidates by leveraging the offline trained model to judge the preference orders. Extensive experiments on the real-world vertical and general community-based question answering datasets have comparatively demonstrated its robustness and promising performance. Also, we have released the codes and data to facilitate other researchers.
Reciprocal regulation of A-to-I RNA editing and the vertebrate nervous system

The fine control of molecules mediating communication in the nervous system is key to adjusting neuronal signaling during development and in maintaining the stability of established networks in the face of altered sensory input. To prevent the culmination of pathological recurrent network excitation or debilitating periods of quiescence, adaptive alterations occur in the signaling molecules and ion channels that control membrane excitability and synaptic transmission. However, rather than encoding (and thus “hardwiring”) modified gene copies, the nervous systems of metazoa have opted for expanding on post-transcriptional pre-mRNA splicing by altering key encoded amino acids using a conserved mechanism of A-to-I RNA editing: the enzymatic deamination of adenosine to inosine. Inosine exhibits similar base-pairing properties to guanosine with respect to tRNA codon recognition, replication by polymerases, and RNA secondary structure (i.e.,: forming-capacity). In addition to recoding within the open reading frame, adenosine deamination also occurs with high frequency throughout the non-coding transcriptome, where it affects multiple aspects of RNA metabolism and gene expression. Here, we describe the recoding function of key RNA editing targets in the mammalian central nervous system and their potential to be regulated. We will then discuss how interactions of A-to-I editing with gene expression and alternative splicing could play a wider role in regulating the neuronal transcriptome. Finally, we will highlight the increasing complexity of this multifaceted control hub by summarizing new findings from high-throughput studies.
PC-Nash: QoS Provisioning Framework With Path-Classification Scheme Under Nash Equilibrium

With a formulated game of non-cooperative internet service providers (ISPs), this paper proposes a new framework for apportioning ISP's responsibility in an end-to-end quality of service (QoS) request. The strategy is based on Path-Classification scheme under Nash equilibrium (PC-Nash), which is obtained by classifying paths according to the quantized QoS level. Optimal QoS-level selection of individual ISP is then captured by the Nash equilibrium. To facilitate the game solution searching, a loss network model is derived for the call acceptance probabilities and the expected utility values. Solutions provided by PC-Nash are compared with three conventional policies, i.e. most-effort (ME), least-effort (LE) and equal-distribution (ED). The reported results show the conformity of call acceptance probabilities between mathematical analysis and discrete-event simulations. Furthermore, with the utility functions of practical service models, ME and LE are found to provide comparable utilities to PC-Nash with respect to peer and retail/wholesale service models, respectively, for a network with the same path quality. However, for networks with different path qualities, PC-Nash outperforms all the conventional policies significantly. From this evidence, PC-Nash is thus expected to be useful in QoS provisioning of practical inter-domain networks.
Craniomandibular signals of diet in adapids.

OBJECTIVES The craniomandibular morphology of the adapid primates of Europe, especially Adapis and Leptadapis (sensu lato), suggests that they possessed enormous jaw adductor muscles. The goal of this study is to estimate jaw adductor muscle mass, physiological cross-sectional area (PCSA), and fiber length in adapid primates from the Eocene of Europe. We also estimated muscle leverage, bite force, and gape parameters. MATERIALS AND METHODS We use bony morphology and osteological correlates of soft tissues in a sample of extant strepsirrhines to estimate these soft-tissue and performance variables in Adapis and Leptadapis. RESULTS Our results suggest that, compared to a broad sample of extant strepsirrhines, Adapis and Leptadapis had relatively great jaw adductor muscle mass, PCSA, and bite force. They had moderately great jaw adductor leverage but no sign of adaptation for wide gapes. There is no support for the hypothesis that either adapid was a gouger. DISCUSSION Our estimates support the inference that Adapis and Leptadapis were primarily folivorous, perhaps also consuming small to medium-sized tough fruits, nuts, and seeds. Explanations for the likely extreme development of the jaw adductor muscles in adapids remain speculative. These include (1) foods that were generally tougher and/or of higher yield strength than those eaten by strepsirrhines today, (2) using the muscles "in shifts" to avoid muscle fatigue in the context of an obdurate diet, and (3) potential constraints on reshaping of the skull for more efficient food processing.
Oligomerization Partially Explains the Lowering of Aβ42 in Alzheimer’s Disease Cerebrospinal Fluid

Background/Objective: The lowering of natively analyzed Aβ42 in cerebrospinal fluid (CSF) is used as a diagnostic tool in Alzheimer’s disease (AD). The presence of Aβ oligomers can interfere with such analyses causing underestimation of Aβ levels due to epitope masking. The aim was to investigate if the lowering of CSF Aβ42 seen in AD is caused by oligomerization. Methods: Aβ42 was analyzed under both denaturing and non-denaturing conditions. An Aβ42 oligomer ratio was calculated from these quantifications. The presence of oligomers leads to Aβ42 epitope masking during non-denaturing assays, resulting in a higher ratio. Results: The Aβ42 oligomer ratio was used for the assessment of oligomerized Aβ in human CSF, after being evaluated in transgenic mouse brain homogenates. AD and mild cognitive impairment (MCI) samples displayed the expected decrease in natively measured Aβ42 compared to healthy controls and frontotemporal dementia, but not when analyzing under denaturing conditions. Accordingly, AD and MCI CSF had a higher Aβ42 oligomer ratio in CSF. Conclusion: Combining denaturing and non-denaturing quantifications of Aβ42 into an oligomer ratio enables the assessment of Aβ oligomers in biological samples. The increased Aβ42 oligomer ratio for AD and MCI indicates the presence of oligomers in CSF and that the lowering of natively measured Aβ42 is caused by oligomerization.
Early Angiosarcoma of the Scalp: A Clinicopathological Pitfall

Abstract:Angiosarcoma (AS) is a rare malignant vascular tumor, which affects mainly elderly patients. After the diagnosis, the mean overall survival of patients is 30 months. The variable presentation of the malignancy, the benign appearance of the cutaneous lesions, and the minimal histological changes in early lesions can sometimes delay the correct diagnosis. The authors report a case of an 80-year-old white male patient, with a painless and ecchymotic lesion of the scalp, which histologically showed minimal pathological atypia, conclusive for a diagnosis of AS with minimal histological changes. The authors discuss the main and most emblematic cases of AS initially misdiagnosed for other cutaneous diseases reported in the literature, noting that in some cases, also the histology can be treacherous and a trap for the dermatopathologist. The recent findings on MYC, FLT4 and KDR amplification, and the relative therapeutic perspectives are also discussed. Finally, the authors draw up some pathological cornerstones, which could improve the diagnosis, above all in early lesions with minimal atypia.
Psychosocial characteristics of women and men attending infertility counselling.

BACKGROUND Little is known about the psychosocial characteristics of infertile couples seeking psychological help. This study describes couples attending infertility counselling. METHODS Questionnaires pertaining to socio-demographic factors, motives for wanting a child, lay aetiology of their infertility, dimensions of life and partnership satisfaction, and a complaints list were completed by 974 women and 906 men. Of those who indicated an openness to counselling, almost half actually attended infertility counselling, and two groups, 'no counselling' (358 women and 292 male partners) and 'taking up counselling' (275 women and 243 male partners), were therefore compared. RESULTS More couples with stressful life events were found in the counselling group. For women taking up counselling, psychological distress, in the form of suffering from childlessness and depression as well as subjective excessive demand (as a potential cause for infertility), was higher in comparison to women not counselled. The higher distress for men in the counselling group was indicated by relative dissatisfaction with partnership and sexuality and by accentuating the women's depression. CONCLUSIONS Infertile couples seeking psychological help are characterized by high levels of psychological distress, primarily in women. The women's distress seems to be more important for attending infertility counselling than that of the men.
Modulatory Effects of Antibody Replacement Therapy to Innate and Adaptive Immune Cells

Intravenous immunoglobulin administered at replacement dosages modulates innate and adaptive immune cells in primary antibody deficiencies (PAD) in a different manner to what observed when high dosages are used or when their effect is analyzed by in vitro experimental conditions. The effects seem to be beneficial on innate cells in that dendritic cells maturate, pro-inflammatory monocytes decrease, and neutrophil function is preserved. The effects are less clear on adaptive immune cells. IVIg induced a transient increase of Treg and a long-term increase of CD4 cells. More complex and less understood is the interplay of IVIg with defective B cells of PAD patients. The paucity of data underlies the need of more studies on patients with PAD before drawing conclusions on the in vivo mechanisms of action of IVIg based on in vitro investigations.
E2F1 and E2F2 induction in response to DNA damage preserves genomic stability in neuronal cells

E2F transcription factors regulate a wide range of biological processes, including the cellular response to DNA damage. In the present study, we examined whether E2F family members are transcriptionally induced following treatment with several genotoxic agents, and have a role on the cell DNA damage response. We show a novel mechanism, conserved among diverse species, in which E2F1 and E2F2, the latter specifically in neuronal cells, are transcriptionally induced after DNA damage. This upregulation leads to increased E2F1 and E2F2 protein levels as a consequence of de novo protein synthesis. Ectopic expression of these E2Fs in neuronal cells reduces the level of DNA damage following genotoxic treatment, while ablation of E2F1 and E2F2 leads to the accumulation of DNA lesions and increased apoptotic response. Cell viability and DNA repair capability in response to DNA damage induction are also reduced by the E2F1 and E2F2 deficiencies. Finally, E2F1 and E2F2 accumulate at sites of oxidative and UV-induced DNA damage, and interact with γH2AX DNA repair factor. As previously reported for E2F1, E2F2 promotes Rad51 foci formation, interacts with GCN5 acetyltransferase and induces histone acetylation following genotoxic insult. The results presented here unveil a new mechanism involving E2F1 and E2F2 in the maintenance of genomic stability in response to DNA damage in neuronal cells.
Predictors of pituitary dysfunction in patients surviving ischemic stroke.

BACKGROUND Stroke is a leading cause of death in industrialized countries, representing the main cause of long-term disability. Recent studies indicate that hypopituitarism may be observed after an acute stroke. OBJECTIVE The aim was to prospectively investigate incidence and pattern of pituitary dysfunction in patients suffering ischemic stroke and to assess the predictive value of different clinical and radiological parameters for hypopituitarism. PATIENTS AND METHODS We assessed endocrine, clinical, radiological, and functional parameters in 56 patients (34 males; mean age, 64.8 ± 1.3 yr; mean body mass index, 25.8 ± 0.45 kg/m(2)) at 1-3 months (visit 1) and 12-15 months (visit 2) after an ischemic stroke. RESULTS At visit 1, hypopituitarism was detected in 20 (35.7%) of 56 stroke patients, with multiple deficits in three and isolated deficits in 17. At visit 2, hypopituitarism was detected in 18 (37.5%) of 48 stroke patients, with multiple deficits in two. Four patients with previously diagnosed isolated GH or LH/FSH deficit exhibited normal pituitary function, whereas GH deficiency was newly diagnosed in three cases. Hypopituitarism was associated with worse outcome. We identified both clinical (preexisting diabetes mellitus, medical complications during hospitalization) and radiological (Alberta Stroke Programme Early CT Score ≤ 7) parameters as major risk factors for developing hypopituitarism after ischemic stroke. CONCLUSIONS Hypopituitarism may associate with ischemic stroke in one third of cases and persist in a long-term period, aggravating the functional outcome. We identified specific risk factors for hypopituitarism after stroke, which may help to select patients needing an accurate endocrine evaluation to improve stroke outcome.
University of Birmingham The influence of stacking fault energy on plasticity mechanisms in triode-plasma nitrided austenitic stainless steels: Implications for the structure and stability of nitrogen-expanded austenite

• Users may freely distribute the URL that is used to identify this publication. • Users may download and/or print one copy of the publication from the University of Birmingham research portal for the purpose of private study or non-commercial research. • User may use extracts from the document in line with the concept of ‘fair dealing’ under the Copyright, Designs and Patents Act 1988 (? ) • Users may not further distribute the material nor use it for the purposes of commercial gain.
L‐ornithine and phenylacetate synergistically produce sustained reduction in ammonia and brain water in cirrhotic rats

Treatment of hyperammonemia and hepatic encephalopathy in cirrhosis is an unmet clinical need. The aims of this study were to determine whether L‐ornithine and phenylacetate/phenylbutyrate (administered as the pro‐drug phenylbutyrate) (OP) combined are synergistic and produce sustained reduction in ammonia by L‐ornithine acting as a substrate for glutamine synthesis, thereby detoxifying ammonia, and the phenylacetate excreting the ornithine‐derived glutamine as phenylacetylglutamine in the urine. Sprague‐Dawley rats were studied 4 weeks after bile duct ligation (BDL) or sham operation. Study 1: Three hours before termination, an internal carotid sampling catheter was inserted, and intraperitoneal saline (placebo), OP, phenylbutyrate, or L‐ornithine were administered after randomization. BDL was associated with significantly higher arterial ammonia and brain water and lower brain myoinositol (P < 0.01, respectively), compared with sham‐operated controls, which was significantly improved in the OP‐treated animals; arterial ammonia (P < 0.001), brain water (P < 0.05), brain myoinositol (P < 0.001), and urinary phenylacetylglutamine (P < 0.01). Individually, L‐ornithine or phenylbutyrate were similar to the BDL group. In study 2, BDL rats were randomized to saline or OP administered intraperitoneally for 6 hours or 3, 5, or 10 days and were sacrificed between 4.5 and 5 weeks. The results showed that the administration of OP was associated with sustained reduction in arterial ammonia (P < 0.01) and brain water (P < 0.01) and markedly increased arterial glutamine (P < 0.01) and urinary excretion of phenylacetylglutamine (P < 0.01) in each of the OP treated groups. Conclusion: The results of this study provide proof of the concept that L‐ornithine and phenylbutyrate/phenylacetate act synergistically to produce sustained improvement in arterial ammonia, its brain metabolism, and brain water in cirrhotic rats. (HEPATOLOGY 2009.)