Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of DNA Bar Codes for Screening of Industrially Important Fungi: the Haplotype of Trichoderma harzianum Sensu Stricto Indicates Superior Chitinase Formation

ABSTRACT Selection of suitable strains for biotechnological purposes is frequently a random process supported by high-throughput methods. Using chitinase production by Hypocrea lixii/Trichoderma harzianum as a model, we tested whether fungal strains with superior enzyme formation may be diagnosed by DNA bar codes. We analyzed sequences of two phylogenetic marker loci, internal transcribed spacer 1 (ITS1) and ITS2 of the rRNA-encoding gene cluster and the large intron of the elongation factor 1-alpha gene, tef1, from 50 isolates of H. lixii/T. harzianum, which were also tested to determine their ability to produce chitinases in solid-state fermentation (SSF). Statistically supported superior chitinase production was obtained for strains carrying one of the observed ITS1 and ITS2 and tef1 alleles corresponding to an allele of T. harzianum type strain CBS 226.95. A tef1-based DNA bar code tool, TrichoCHIT, for rapid identification of these strains was developed. The geographic origin of the strains was irrelevant for chitinase production. The improved chitinase production by strains containing this haplotype was not due to better growth on N-acetyl-β-d-glucosamine or glucosamine. Isoenzyme electrophoresis showed that neither the isoenzyme profile of N-acetyl-β-glucosaminidases or the endochitinases nor the intensity of staining of individual chitinase bands correlated with total chitinase in the culture filtrate. The superior chitinase producers did not exhibit similarly increased cellulase formation. Biolog Phenotype MicroArray analysis identified lack of N-acetyl-β-d-mannosamine utilization as a specific trait of strains with the chitinase-overproducing haplotype. This observation was used to develop a plate screening assay for rapid microbiological identification of the strains. The data illustrate that desired industrial properties may be an attribute of certain populations within a species, and screening procedures should thus include a balanced mixture of all genotypes of a given species.
A case of tinnitus induced by chlorpromazine in a pediatric patient

Chlorpromazine is a well-known antipsychotic agent that binds with a variety of receptors in the central nervous system. To date, chlorpromazine has never been associated with onset of hearing disorders and tinnitus. We report on an unexpected suspect adverse reaction to chlorpromazine that occurred in a 12-year-old boy, affected by severe generalized anxiety disorder. After treatment with chlorpromazine, the patient experienced an enhanced sensitivity to sounds accompanied by perception of noises of the buzzing or ringing type. This clinical case is of great clinical interest as chlorpromazine is not currently included among potentially ototoxic drugs.
Ibudilast (AV-411)

The treatment of neuropathic pain is a major unresolved medical challenge. Present pharmacotherapies only have modest efficacy and numerous side effects. The use of opioid analgesics is additionally coupled with dependence and withdrawal syndromes. Ibudilast (AV-411) is a non-selective phosphodiesterase inhibitor that is also known to suppress glial cell activation. It has been used clinically for other indications with a good safety profile. As glial cell activation is considered to crucially contribute to neuropathic pain as well as opioid dependence and withdrawal, the authors conceived that ibudilast may be useful for treating these conditions. Preclinical data indicate that ibudilast crosses the blood–brain barrier, is well tolerated, is active on oral administration, reduces glial activation and attenuates pain symptoms in diverse rat models of neuropathic pain. In addition, it enhances acute morphine analgesia and attenuates morphine tolerance and withdrawal. Thus ibudilast may improve opioid efficacy and is a promising therapeutic candidate for neuropathic pain, with a novel mechanism of action.
Weaver, an automatic texture builder

Given in input a 3D digital model of a real object and a set of images from different view points, the problem considered is how to build a single texture map which integrates the color info contained in the input images, minimizing redundancy and optimizing the color attribute representation. We improve a previous solution (which stitches the images on the geometry) by introducing a new approach for a better color matching of the different adjoining texture chunks. The new solution applies cross-correlation and interpolation of the input images directly on the texture image space. Our averaging technique can remove color difference or discontinuity between adjacent sections of the 3D models which are mapped on different input images; in particular, the process is performed on the whole texture, contrary to other approaches that limit color smoothing on small transition zones.
Detection of CK-19 mRNA-positive cells in the peripheral blood of breast cancer patients with histologically and immunohistochemically negative axillary lymph nodes.

BACKGROUND To investigate the incidence of direct hematogenous spread of cancer cells in patients with early-stage breast cancer by studying the presence of occult tumor cytokeratin-19 (CK-19) mRNA(+) cells in the peripheral blood in relation to the status of sentinel (SLNs) and (ALNs) axillary lymph nodes. PATIENTS AND METHODS SLNs and ALNs from 111 patients with operable stage I-II breast adenocarcinoma were evaluated for the presence of tumor cells by hematoxylin-eosin (H&E) staining and, if negative, by immunohistochemistry (IHC) using an anti-CK-19 antibody. Peripheral blood was also analyzed for the presence of CK-19 mRNA(+) cells by nested RT-PCR, before the initiation of adjuvant treatment and in CK-19 mRNA(+) patients following the completion of adjuvant chemotherapy and hormonal treatment. RESULTS After both H&E staining and IHC analysis, 29 (26%) patients were ALN negative (N0). In 78 (70%) patients H&E staining and in four (3.6%) IHC analysis revealed tumors cells, and these patients were considered as ALN positive (N+). Peripheral blood CK-19 mRNA(+) cells were detected in nine (31%) out of 29 N0 and in 31 (38%) out of 82 N + patients (P=0.5) before any adjuvant treatment. Adjuvant chemotherapy and hormone treatment resulted in the disappearance of the CK-19 mRNA(+) cells in all N0 patients and in 15 out of 31 N + patients. After a median follow-up of 40 months, all the N0 CK-19 mRNA(+) patients were relapse-free whereas four (13%) N + CK-19 mRNA(+) patients had relapsed. CONCLUSIONS Direct hematogenous dissemination of occult tumor cells may occur in a substantial proportion of patients with early-stage breast cancer. The prognostic implication of the detection of these cells requires long follow-up periods and further studies.
Identification system for smart homes using footstep sounds

This work proposes an identification system for smart buildings using footstep information. Basically, the system has three modules: pre-processing, feature extraction and selection, and classification of the information. Gait frequency, spectral envelope, cepstral and mel-cepstral analysis and loudness compose the set of parameters used to identify subjects in the smart building. In order to select features, the Fisher's criterion was used. For the classification task, K-Means and K-NN algorithms were performed along with different methodologies for test and validation. Moreover, the best sets were gathered, increasing the accuracy of classification. Several experiments were performed with 15 subjects wearing 6 different footwear. The classification rates were in the range from 33.5% to 97.5%.
Power converters and its application in electric traction systems. Analysis Present and Future Technologies

The traction systems for electric vehicles have advanced considerably over recent years, with the application of different topologies of power converters for the control of various types of electric induction motors and permanent magnet. Furthermore, the evolution of power semiconductor elements of Si to SiC wideband have opened up lines of research and development in this area. The trend of manufacturer's traction systems is to reach compact systems where the power dissipation is high and the reduction of losses is minimal, for it the implementation of topologies of converters with SiC devices seems to be a good alternative of use to improve the performance of these systems This paper describes a study and review of the different types of converter topologies proposed for the development and application in traction systems for electric vehicles. This review will identify the different works presented and analyze their problems, with the aim of seek to optimize these topologies or propose new types of topologies for implementation in traction systems.
Quantitation of response to therapy in patients with metastatic breast carcinoma by serial analysis of plasma gross cystic disease fluid protein and carcinoembryonic antigen

The maximum percent change (MPC) of plasma carcinoembryonic antigen (CEA) and gross cystic disease fluid protein (CDP) were correlated with response to therapy in 92 metastatic breast carcinoma patients. In patients treated with hormone therapy MPC values were significantly different between patients with disease progression (Prog) and regression (Reg): MPC‐CEA for Reg = −72 ± 7%, for Prog = 396 ± 150%; MPC‐CDP for Reg = −86 ± 6%, for Prog = 702 ± 330%, P > 0.001 in a one‐way ANOVA for CEA and CDP. Similar differences were noted in patients treated with chemotherapy. Decreased (>50%) plasma CEA levels were observed in 24/29 (83%) of Reg, 18/35 (51%) stable and 0/49 (0%) of Prog; decreased (>50%) plasma CDP levels were noted in 19/24 (79%) of Reg, 21/28 (75%) of stable and 2/35 (6%) of Prog. Patients with plasma marker decreases > 50% had significantly longer responses to therapy (14.2 months for CEA, 14.1 months for CDP) compared to patients with < 20% decrease (2.0 months for CEA, 0.8 months for CDP), P < 0.001 in a one‐way ANOVA. Decreasing marker levels during the initial six weeks of therapy (negative slope) accurately identified Reg or stable patients: the predictive value of a negative slope was 92% for CEA and 86% for CDP. Rising marker values correctly identified treatment failures (Prog): the predictive value of a positive slope was 90% for CEA and 76% for CDP. These data indicated that changes in plasma CEA and CDP levels reflected increasing or decreasing tumor burden during hormone or chemotherapy treatment of metastatic breast carcinoma. Criteria have been established to predict therapeutic outcome based on the slope of CEA or CDP after six weeks of treatment.
Intellectual outcome after reduced-dose radiation therapy plus adjuvant chemotherapy for medulloblastoma: a Children's Cancer Group study.

PURPOSE To investigate the intellectual outcomes of children with medulloblastomas/primitive neuroectodermal tumors (MB/PNET) treated with reduced-dose craniospinal radiotherapy (RT) plus adjuvant chemotherapy. PATIENTS AND METHODS Forty-three children with average-risk posterior fossa MB/PNETs underwent longitudinal intelligence testing. All had been treated with a reduced-dose craniospinal RT regimen (23.4 Gy to the neuraxis, 32.4-Gy boost to the posterior fossa) and adjuvant chemotherapy. RESULTS The estimated rate of change from baseline was significant for Full Scale Intelligence Quotient (FSIQ), Verbal IQ (VIQ), and Nonverbal IQ (NVIQ) (P <.001 for all three outcomes). The rate of change was estimated to be -4.3 FSIQ points per year, -4.2 VIQ points per year, and -4.0 NVIQ points per year. Females were more subject to VIQ decline than were males (P =.008), and young children (< 7 years of age) were more negatively affected than were older children, with a significant decline in NVIQ (P =.016). Finally, patients with higher baseline evaluations suffered greater declines in IQ than did those with lower baseline scores. CONCLUSION This study represents the largest series of patients with average-risk MB/PNETs treated with a combination of reduced-dose RT and adjuvant chemotherapy whose intellectual development has been followed prospectively. Intellectual loss was substantial but suggestive of some degree of intellectual preservation compared with effects associated with conventional RT doses. However, this conclusion remains provisional, pending further research.
Immunogenicity and Tolerability of Intradermal Administration of an HCV E1-Based Vaccine Candidate in Healthy Volunteers and Patients with Resolved or Ongoing Chronic HCV Infection

The tolerability and immunogenicity of intradermal injections of a candidate HCV vaccine, based on the E1 protein of the hepatitis C virus (HCV), was examined in an exploratory study in healthy volunteers, in subjects with a history of resolved HCV infection, and in patients suffering from therapy-resistant chronic HCV. Sub-epidermal injection of three doses of 4 µg of non-adjuvanted E1 vaccine induced much weaker humoral and cellular immune responses in healthy subjects and chronic HCV patients than the intramuscular administration of 20 µg E1 formulated on alum. However, in three subjects who cleared HCV infection, intradermal administration of this low dose of E1 induced rapid and clear anamnestic responses. These data demonstrate that E1-specific immune responses can be induced in resolving HCV infections and that memory (B and T) cells can be restimulated with suboptimal doses of E1 antigen.
Aspects on human amyloid forms and their fibril polypeptides

Amyloid is an in vivo fibrillar substance containing a fibril protein and several additional molecules. Presently, 25 proteins have been reported as main fibril components. Why just a few proteins form amyloid in vivo is still insufficiently understood. Many fibril proteins appear as fragments of larger precursors and for some types it is not clear whether fragmentation comes before or after fibrillation. The self‐assembly by amyloid proteins can be speeded up by seeding with preformed fibrils. In mice, systemic amyloidoses are transmissible by a seeding mechanism. Whether this prion‐like mechanism occurs in humans is not known, but can definitely not be ruled out.
Sequence specificity of the core-binding factor

The core-binding factor (CBF) binds the conserved core motif in mammalian type C retrovirus enhancers. We analyzed the phosphate contacts made by CBF on the Moloney murine leukemia virus enhancer by ethylation interference assay. The phosphate contacts span 9 bp centered around the consensus core site. To examine the sequence preferences for CBF binding, we employed the technique of selected and amplified binding sequence footprinting (T. K. Blackwell and H. Weintraub, Science 250:1104-1110, 1990). The consensus binding site for CBF defined by selected and amplified binding sequence footprinting is PyGPyG GTPy.
In vivo adriamycin-induced apoptosis in peritoneal murine macrophages: partial participation of a caspase cascade.

BACKGROUND Adriamycin (ADM) is a potent antitumor drug that induces apoptosis (AP) in tumor cells. AP is modulated by caspases and by mitogen-activated protein kinases (MAPK) as well as by the mitochondrial membrane potential (deltapsim). We studied the participation of these systems in peritoneal macrophages from ADM-treated mice. MATERIALS AND METHODS Balb/c mice were either treated with ADM (5 mg/kg, i.p.) or with 0.85% NaCl solution (controls). One hour later, peritoneal cells were harvested and cultured for 28 h. AP was evaluated by ethidium bromide and acridine orange staining; deltapsim was monitored using a MitoCapture stain Kit; DNA integrity was assessed by electrophoretic analysis. Animals were treated (i.p.) 1 h before ADM administration with Z-LEHD-FMK, Z-DEVD-FMK, or Z-VAD-FMK (caspase-9, caspases-3, 7,10 and general caspase inhibitors, respectively) or with PD169316 (a MAPKp38 inhibitor). RESULTS ADM induced a higher rate of AP and the characteristic electrophoretic DNA ladder pattern. Mice treated with caspases inhibitors plus ADM showed significant reductions in AP and DNA laddering; in contrast, no differences were observed in mice treated with PD169316 plus ADM in comparison with ADM alone. ADM also induced early loss of the deltapsim. CONCLUSION In these experimental conditions, ADM induced AP in a mainly caspase-9-dependent manner and this was related to a reduction in the deltapsim.
Novel type of genetic rearrangement in the iduronate‐2‐sulfatase (IDS) gene involving deletion, duplications, and inversions

We describe a novel type of complex genetic rearrangement in the iduronate‐2‐sulfatase (IDS) gene of a severely affected MPSII patient. Southern blot analysis indicated an intragenic deletion of exons 5 and 6. The deletion spans 5,581 bp. Sequencing of the deletion junctions revealed a complex rearrangement involving duplications and inversions. A remaining 20 bp fragment (c) from the intron 6 sequence and two duplicated IDS gene fragments of 314 bp (a) from intron 6/exon 7 boundary and 23 bp (b) from exon 7 were found between the deletion breakpoints. Fragments a and c were placed in an inverted orientation. We suggest that the described rearrangement is a result of a nonhomologous recombination event at sites with little homology. The proposed model explaining this recombinational event involves the formation of “tetra‐loop” single‐stranded DNA structure during replication. The complexity of the described rearrangement and the lack of large homologous sequences at the mutational breakpoints suggest that complex molecular intermediates are formed during illegitimate recombination. Hum Mutat 14:471–476, 1999. © 1999 Wiley‐Liss, Inc.
Endogenous concentrations, pharmacokinetics, and selected pharmacodynamic effects of a single dose of exogenous GABA in horses.

The anti-anxiety and calming effects following activation of the GABA receptor have been exploited in performance horses by administering products containing GABA. The primary goal of the study reported here was to describe endogenous concentrations of GABA in horses and the pharmacokinetics, selected pharmacodynamic effects, and CSF concentrations following administration of a GABA-containing product. The mean (±SD) endogenous GABA level was 36.4 ± 12.5 ng/mL (n = 147). Sixteen of these horses received a single intravenous and oral dose of GABA (1650 mg). Blood, urine, and cerebrospinal fluid (n = 2) samples were collected at time 0 and at various times for up to 48 h and analyzed using LC-MS. Plasma clearance and volume of distribution was 155.6 and 147.6 L/h and 0.154 and 7.39 L for the central and peripheral compartments, respectively. Terminal elimination half-life was 22.1 (intravenous) and 25.1 (oral) min. Oral bioavailability was 9.81%. Urine GABA concentrations peaked rapidly returning to baseline levels by 3 h. Horses appeared behaviorally unaffected following oral administration, while sedative-like changes following intravenous administration were transient. Heart rate was increased for 1 h postintravenous administration, and gastrointestinal sounds decreased for approximately 30 min following both intravenous and oral administration. Based on a limited number of horses and time points, exogenously administered GABA does not appear to enter the CSF to an appreciable extent.
Working through the issues: how issue diversity and ideological disagreement influence coalition duration

Issue salience and diversity direct a range of outcomes such as voting behavior and public policy. Studies, however, have yet to fully integrate theoretical or empirical expectations for the effect of issue salience on coalition stability. By focusing on the mechanism linking parties’ preferences to policy-making, I propose that parties with more diverse platforms provide coalitions greater room to negotiate, whereas parties focusing on a small number of issues exacerbate ideological tensions. Issue diversity becomes important once parties exhaust opportunities to make the initial, easy policy compromises. Using evidence from 299 coalitions in 24 European countries, I find that issue diversity in parties’ platforms moderates the effect of disagreement. Using a non-proportional hazard analysis, I find that the effect of issue diversity varies over the coalition’s lifecycle. Governments with parties willing to negotiate over a larger range of issues decrease the risk that disagreements will result in coalition termination.
Expressing pain and fatigue: a new method of analysis to explore differences in osteoarthritis experience.

OBJECTIVE To apply a new method of analysis to 2 large qualitative datasets in order to examine differences in osteoarthritis (OA) experience according to the affected joint (knee or hip) and sex. METHODS A secondary analysis of qualitative data from 2 studies was conducted. Study 1 comprised 28 focus groups with 50 men and 80 women (ages 47-92 years). Study 2 comprised 14 focus groups with 32 men and 56 women (ages 56-91 years). All participants had symptomatic OA. In Study 1, secondary analysis using comparative keyword analysis (CKA) compared relative frequencies of words uttered by participants experiencing knee pain with words used by participants experiencing hip pain. In Study 2, CKA compared words used by men with words used by women. Subsequent analysis explored the contexts in which participants used key words. RESULTS All participants in Study 1 described concerns with their bodies, activity limitations, and pain management, but details of their concerns differed. People with knee pain focused on stairs, weight, and stiffness, while those with hip pain were concerned with sidedness and groin pain. In Study 2, both men and women discussed activity and interaction with spouses. However, men used more factual words, especially relating to enumeration, while women offered more explanation without prompting from others. CONCLUSION CKA provides productive inroads into qualitative datasets. Understanding the different ways that affected joints are discussed, and sex differences in descriptions of OA, may lead to improvements in clinical assessment tools, better targeting of interventions, and enhanced communication between health care professionals and patients.
A Novel HARQ Using Grouping and Encoding Technique

In this paper, a novel HARQ scheme is proposed by grouping the information bit portion from failed packet and the new information bit portion from new transmit packet, and then both portions are encoded by CRC and turbo code. In the reception, both bit portions are jointly decoded to obtain grouped HARQ coding gain. System level simulation demonstrates that grouping based HARQ achieves 15% sector throughput gain as opposed to conventional Chase-combining HARQ by slightly suffering transmit latency and only adding an ACK/NAK bit.
Comparison of three magnet array-type rotors in surface permanent magnet-type vernier motor

Surface permanent magnet-type vernier motors with three magnet array-type rotors (parallel magnetized type, repulsion type, and Halbach type) are compared based on the pull-out torque. It was clarified that increasing the rotor radius increases the pull-out torque at a fixed three-phase alternating voltage. The mechanism for the pull-out torque increase on each magnet array type was different, when the effects of the increase were analyzed based on an induced electromotive force and a synchronous reactance. As a result, the design of the Halbach-type rotor was found to be especially effective for achieving high pull-out torque, because this array type achieves a large induced electromotive force E0 and a small synchronous reactance xs.