Miracle-dz/UniFAR-FTUs huggingface dataset:
Tenebrio molitor Gram‐negative‐binding protein 3 (TmGNBP3) is essential for inducing downstream antifungal Tenecin 1 gene expression against infection with Beauveria bassiana JEF‐007

The Toll signaling pathway is responsible for defense against both Gram‐positive bacteria and fungi. Gram‐negative binding protein 3 (GNBP3) has a strong affinity for the fungal cell wall component, β‐1,3‐glucan, which can activate the prophenoloxidase (proPO) cascade and induce the Toll signaling pathway. Myeloid differentiation factor 88 (MyD88) is an intracellular adaptor protein involved in the Toll signaling pathway. In this study, we monitored the response of 5 key genes (TmGNBP3, TmMyD88, and Tenecin 1, 2, and 3) in the Toll pathway of the mealworm Tenebrio molitor immune system against the fungus Beauveria bassiana JEF‐007 using RT‐PCR. TmGNBP3, Tenecin 1, and Tenecin 2 were significantly upregulated after fungal infection. To better understand the roles of the Toll signaling pathway in the mealworm immune system, TmGNBP3 and TmMyD88 were knocked down by RNAi silencing. Target gene expression levels decreased at 2 d postknockdown and were dramatically reduced at 6 d post‐dsRNA injection. Therefore, mealworms were compromised by B. bassiana JEF‐007 at 6 d post‐dsRNA injection. Silencing of TmMyD88 and TmGNBP3 resulted in reduced resistance of the host to fungal infection. Particularly, reducing TmGNBP3 levels obviously downregulated Tenecin 1 and Tenecin 2 expression levels, whereas silencing TmMyD88 expression resulted in decreased Tenecin 2 expression. These results indicate that TmGNBP3 is essential to induce downstream antifungal peptide Tenecin 1 expression against B. bassiana JEF‐007.
Cotranslational Folding of Globin*

Globin synthesis in a wheat germ cell-free translation system was performed in the presence of [3H]hemin and [35S]methionine to determine the minimal length of the nascent ribosome-bound globin chain capable of heme binding. Nascent polypeptides of predetermined size were synthesized on ribosomes by translation of truncated mRNA molecules. Analysis with the use of sucrose gradient centrifugation and puromycin reaction revealed that the ribosome-bound N-terminal α-globin fragments of 140, 100, and 86 amino acid residues are capable of an efficient heme binding, whereas those of 75, 65, and 34 amino acid residues display a significantly weaker, or just nonspecific, affinity to heme. This indicates that the ribosome-bound nascent chain of 86 amino acid residues has already acquired a spatial structure that allows its interaction with the heme group or that heme attachment promotes the formation of the proper tertiary structure in the ribosome-bound nascent peptide. In any case the cotranslational folding of globin is suggested.
Building a Theoretical Framework to Link Local Taxes and Parental Choice of Education

This paper theoretically examines the link between local taxes and education choice (indicated by private school enrollment rate or public school enrollment rate). The evidence shows that local taxes and parental choice of education are endogenously determined by one another. More importantly, this study frames an economic theoretical background for local taxes and parental choice of education, which can be useful in constructing empirical models for further investigations of this issue.
A high proportion of founder BRCA1 mutations in Polish breast cancer families

Three mutations in BRCA1 (5382insC, C61G and 4153delA) are common in Poland and account for the majority of mutations identified to date in Polish breast and breast–ovarian cancer families. It is not known, however, to what extent these 3 founder mutations account for all of the BRCA mutations distributed throughout the country. This question has important implications for health policy and the design of epidemiologic studies. To establish the relative contributions of founder and nonfounder BRCA mutations, we established the entire spectrum of BRCA1 and BRCA2 mutations in a large set of breast–ovarian cancer families with origins in all regions of Poland. We sequenced the entire coding regions of the BRCA1 and BRCA2 genes in 100 Polish families with 3 or more cases of breast cancer and in 100 families with cases of both breast and ovarian cancer. A mutation in BRCA1 or BRCA2 was detected in 66% of breast cancer families and in 63% of breast–ovarian cancer families. Of 129 mutations, 122 (94.6%) were in BRCA1 and 7 (5.4%) were in BRCA2. Of the 122 families with BRCA1 mutations, 119 (97.5%) had a recurrent mutation (i.e., one that was seen in at least 2 families). In particular, 111 families (91.0%) carried one of the 3 common founder mutations. The mutation spectrum was not different between families with and without ovarian cancer. These findings suggest that a rapid and inexpensive assay directed at identifying the 3 common founder mutations will have a sensitivity of 86% compared to a much more costly and labor‐intensive full‐sequence analysis of both genes. This rapid test will facilitate large‐scale national epidemiologic and clinical studies of hereditary breast cancer, potentially including studies of chemoprevention. © 2004 Wiley‐Liss, Inc.
Diagnostic specificity, sensitivity and cross-reactivity of an enzyme-linked immunosorbent assay for the detection of antibody against Leptospira interrogans serovars pomona, sejroe and hardjo in cattle.

Outer sheath antigen was prepared from Leptospira interrogans serovars pomona, sejroe and hardjo by treating the organisms with 1.0M NaC1 followed by 0.04% sodium dodecyl sulfate (SDS). Sodium dodecyl sulfate was removed from the SDS-protein complexes by the extraction of dodecyl sulfate anions as ion pairs with triethylammonium cations into an organic solvent. The outer sheath antigen was recovered from the organic solvent as a precipitate and used as the source of leptospiral enzyme-linked immunosorbent assay (ELISA) antigen. Utilizing this antigen, ELISA was adapted to detect bovine serum antibody to L. interrogans serovars pomona, sejroe and hardjo. The specificity of this assay in 344 bovine sera, which were negative in the microscopic agglutination test (MAT) for seven serovars, was 99.4%. In sera from 37 and 87 cattle which revealed MAT titers greater than or equal to 1:50 for L. interrogans serovars pomona and sejroe, the relative sensitivity of the test was 100%. The ELISA also showed a considerable degree of low level cross-reactivity with other serovars. Sixty-six (75.9%) out of 87 bovine sera which were MAT-positive (MAT titer of greater than or equal to 1:50) with serovars sejroe and hardjo only were ELISA positive with heterologous pomona antigen; 16 (43.2%) and six 16.2%) out of 37 bovine sera which were MAT positive MAT titer of greater than or equal to 1:50) with serovar pomona only were ELISA positive with heterologous sejroe and hardjo ELISA antigen respectively. (ABSTRACT TRUNCATED AT 250 WORDS)
The Tomato odorless-2 Mutant Is Defective in Trichome-Based Production of Diverse Specialized Metabolites and Broad-Spectrum Resistance to Insect Herbivores1[W][OA]

Glandular secreting trichomes of cultivated tomato (Solanum lycopersicum) produce a wide array of volatile and nonvolatile specialized metabolites. Many of these compounds contribute to the characteristic aroma of tomato foliage and constitute a key part of the language by which plants communicate with other organisms in natural environments. Here, we describe a novel recessive mutation called odorless-2 (od-2) that was identified on the basis of an altered leaf-aroma phenotype. od-2 plants exhibit pleiotrophic phenotypes, including alterations in the morphology, density, and chemical composition of glandular trichomes. Type VI glandular trichomes isolated from od-2 leaves accumulate only trace levels of monoterpenes, sesquiterpenes, and flavonoids. Other foliar defensive compounds, including acyl sugars, glycoalkaloids, and jasmonate-regulated proteinase inhibitors, are produced in od-2 leaves. Growth of od-2 plants under natural field conditions showed that the mutant is highly susceptible to attack by an indigenous flea beetle, Epitrix cucumeris, and the Colorado potato beetle, Leptinotarsa decemlineata. The increased susceptibility of od-2 plants to Colorado potato beetle larvae and to the solanaceous specialist Manduca sexta was verified in no-choice bioassays. These findings indicate that Od-2 is essential for the synthesis of diverse trichome-borne compounds and further suggest that these compounds influence host plant selection and herbivore community composition under natural conditions.
MLPA: a rapid, reliable, and sensitive method for detection and analysis of abnormalities of 22q

In this study, essential test characteristics of the recently described multiplex ligation‐dependent probe amplification (MLPA) method are presented, using chromosome 22 as a model. This novel method allows the relative quantification of ∼40–45 different target DNA sequences in a single reaction. For the purpose of this study, MLPA was performed in a blinded manner on a training set containing over 50 samples, including typical 22q11.2 deletions, various atypical deletions, duplications (trisomy and tetrasomy), and unbalanced translocations. All samples in the training set have been previously characterized by fluorescence in situ hybridization (FISH) with cosmid or BAC clones and/or cytogenetic studies. MLPA findings were consistent with cytogenetic and FISH studies, no rearrangement went undetected and repeated tests gave consistent results. At a relative change in comparative signal strength of 30% or more, sensitivity and specificity values were 0.95 and 0.99, respectively. Given that MLPA is likely to be used as an initial screening method, a higher sensitivity, at the cost of a lower specificity, was deemed more appropriate. A receiver operator characteristic (ROC) curve analysis was performed to calculate the most optimal threshold range, with associated sensitivity and specificity values of 0.99 and 0.97, respectively. Finally, performance of each individual probe was analyzed, providing further useful information for the interpretation of MLPA results. In conclusion, MLPA has proven to be a highly sensitive and accurate tool for detecting copy number changes in the 22q11.2 region, making it a fast and economic alternative to currently used methods. The current study provides valuable and detailed information on the characteristics of this novel method. Hum Mutat 27(8), 814–821, 2006. Published 2006 Wiley‐Liss, Inc.
Endogenous N‐losses in broilers estimated by a [15N]‐isotope dilution technique: Effect of dietary fat type and xylanase addition

Male broilers were given a low protein diet (15.5% CP) spiked with [15N]H4HCO3 from day 12 to day 18 of age to label the endogenous N‐constituents. Experimental diets were subsequently fed from day 19 to day 24 of age and consisted of a rye based diet (56% dietary inclusion) which contained either 10% soya oil (S) or 10% beef tallow (T), each of which was either unsupplemented (‐) or supplemented (+) with a xylanase containing enzyme preparation (2700 IU/kg at pH 5.3). [15N]‐atom percent excess (APE) of excreta, faeces and urine were monitored on a daily basis during both experimental periods. Furthermore, APE was measured in various tissues at the end of the experiment. The APE of urine on the last day of the experiment was between the APE of the pancreas and that of the jejunal tissue, an observation which supported the usefulness of using urinary APE as an indicator for the endogenous N‐pool. Endogenous N‐proportions were estimated by an isotope dilution technique at the end of the experiment by examination of the ratio of APE in faeces and urine. The endogenous N‐proportion in the faeces was greatest in birds receiving the T(‐) diet. The proportions were 0.321, 0.319, 0.451 and 0.289 in S(‐), S(+), T(‐) and T(+) fed groups, respectively. Xylanase addition reduced endogenous N‐proportion, a factor which was used to correct apparent crude protein digestibility (85.6, 86.2, 84.3 and 88.5% in S(‐), S(+), T(‐) and T(+) fed birds, respectively) for endogenous losses resulting in almost equal true digestibilities of crude protein for all treatments (90.3, 90.6, 90.4 and 91.5%). The amounts of endogenous N in faces were estimated to be 87, 69, 244 and 81 mg per day per kg0.67 body weight in S(‐), S( + ), T(‐) and T( + ) fed birds, respectively. It was concluded that xylanase supplementation of a rye based broiler diet does not change endogenous N‐secretions when the supplemental fat is soya oil. However, addition of tallow rather than soya oil increased these N‐losses significantly, an effect which was reversed by xylanase addition.
Persistence of muscle catabolism after severe burn.

BACKGROUND The hypermetabolic response to severe burn is characterized by muscle protein catabolism. Current opinion states that the hypermetabolic state resolves soon after complete wound closure. Clinically, we have witnessed that burned children appear to be hypermetabolic and catabolic long after full healing of their wounds. Our goal in this study was to determine scientifically if burn-associated hypermetabolism persists after full wound healing. METHODS To determine the duration of muscle catabolism and systemic hypermetabolism after severe burn in children, patients with > 40% total body surface area burns were enrolled in a prospective, longitudinal study; resting energy expenditure was measured by indirect calorimetry, muscle protein kinetics were determined by using stable isotopic methodology, and body composition was measured by dual-energy x-ray absorptiometry imaging. Data were collected at 6, 9, and 12 months after injury. RESULTS The mean total body surface area burned was 65% +/- 13%, and the mean age was 7.6 +/- 1. 5 years. Resting energy expenditure was elevated above the predicted age-matched levels from the Harris-Benedict equation and incrementally declined throughout the 12-month study. The net protein balance and lean mass reflected catabolic persistence at 6 and 9 months after severe burn. Between 9 and 12 months, protein breakdown decreased, net protein balance improved, and lean body mass increased. CONCLUSIONS In severely burned children, hypermetabolism and catabolism remain exaggerated for at least 9 months after injury. This suggests that therapeutic attempts to manipulate the catabolic and hypermetabolic response to severe injury should be continued long after injury.
Does the Patient's Payer Matter in Hospital Patient Safety?: A Study of Urban Hospitals

Background:Previous studies have documented that hospitals decrease costs in response to reimbursement cutbacks. However, research concerning how this may affect quality of care has produced mixed results. Until recently, the ability to study changes in patient safety and payment has been limited. Objective:The objective of the study was to determine whether changes in 4 hospital patient safety indicator (PSI) rates are related to changes in the generosity of payers over time. Data and Methods:Study data are drawn from 1995–2000 hospital discharges in 11 states in the Agency for Healthcare Research and Quality Healthcare Cost and Utilization Project State Inpatient Database. Following the same organizations over time, we estimate hospital fixed-effects regression models of the association of payer-specific time and post Balanced Budget Act (BBA) payment changes with risk-adjusted hospital PSI rates controlling for patient, organizational, and market characteristics. Four PSIs relevant to a large number of patients and hospitals that reflect general care processes are studied. Results:The time trend during 1995–2000 is consistently significantly positive for private and Medicare hospital PSI rates. Thus, after controlling for patient characteristics and organizational and market factors, performance worsened. The trend is less consistent for Medicaid and does not exist for self-pay hospital PSI rates. After adjusting for multiple comparisons, we also find that the Medicare trend is fairly consistently higher than that of the other payers. In contrast, there is a less consistent BBA effect, especially for Medicare.
Professional Development School Triads Inquiring about Student Work in Elementary Mathematics.

This article reports on a case of cross-role triads (mentor, intern, and supervisor) in a professional development school (PDS) setting engaged in the process of looking at student work in elementary mathematics over time. The study represents a significant effort to understand what inquiryoriented behavior looks like in this context. By recognizing and understanding these behaviors, new insights are gained about the development of an inquiry stance. The primary source of data was audiorecorded triad meetings, which were analyzed for observable inquiry-oriented behaviors in practice. It was found that each triad exhibited distinctive patterns of talk about mathematical knowledge, student understandings, and instructional practice. Moreover, each triad’s talk also displayed a unique orientation toward inquiry. The findings from this study have implications for developing pre-service university-based training experiences and providing recommendations to school district leaders regarding meaningful professional development for collaborative groups examining student work. NAPDS Essentials Addressed: #4/A shared commitment to innovative and reflective practice by all participants; #5/ Engagement in and public sharing of the results of deliberate investigations of practice by respective participants; #7/A structure that allows all participants a forum for ongoing governance, reflection, and collaboration.
Imaging of hepatic hemangiomas using multirotation dynamic SPECT

Hepatic hemangiomas are benign vascular lesions with 3 to 7% prevalence in the population, often appearing as suspicious masses during CT or ultrasound examination. Diagnosis through nuclear medicine relies heavily on the acquisition of a characteristic temporal uptake of Tc99m-labelled red blood cells in the lesion. Dynamic SPECT (dSPECT), a unique reconstruction method that generates a temporal series of 3D images, may potentially improve upon the 2D planar imaging currently used to capture dynamic behavior. A Monte-Carlo simulation of the digital NCAT phantom with a simulated liver hemangioma of increasing activity was used to generate 640 projections with and without scatter over 5 rotations of a dual-headed gamma camera. The dSPECT was used to reconstruct the 5-rotation projection data set, generating 80 frames in total. Also, the 5 rotations were divided into 5, 360/spl deg/ data sets and reconstructed with a static rescaled-block-iterative (RBI) method with and without attenuation correction for comparison. Clinical feasibility was also assessed. The clinical protocol consists of 1.5-min of planar dynamic imaging, four 5-min SPECTs, and a final 30-min SPECT with transmission imaging to provide a patient-specific attenuation map. The four 5-min SPECTs were reconstructed both as 4 separate static images using the RBI method with and without attenuation correction, and as a single dynamic series using the dSPECT algorithm in order to compare each technique's ability to provide dynamic information. The dSPECT reproduces the simulated activity accurately. Regional TACs can be generated from multiple slow-rotation dynamic SPECT acquisitions and could be used in the diagnosis of hemangioma.
Phylogenetic Evidence for the Existence of Novel Thermophilic Bacteria in Hot Spring Sulfur-Turf Microbial Mats in Japan

ABSTRACT So-called sulfur-turf microbial mats, which are macroscopic white filaments or bundles consisting of large sausage-shaped bacteria and elemental sulfur particles, occur in sulfide-containing hot springs in Japan. However, no thermophiles from sulfur-turf mats have yet been isolated as cultivable strains. This study was undertaken to determine the phylogenetic positions of the sausage-shaped bacteria in sulfur-turf mats by direct cloning and sequencing of 16S rRNA genes amplified from the bulk DNAs of the mats. Common clones with 16S rDNA sequences with similarity levels of 94.8 to 99% were isolated from sulfur-turf mat samples from two geographically remote hot springs. Phylogenetic analysis showed that the phylotypes of the common clones formed a major cluster with members of theAquifex-Hydrogenobacter complex, which represents the most deeply branching lineage of the domain bacteria. Furthermore, the bacteria of the sulfur-turf mat phylotypes formed a clade distinguishable from that of other members of theAquifex-Hydrogenobacter complex at the order or subclass level. In situ hybridization with clone-specific probes for 16S rRNA revealed that the common phylotype of sulfur-turf mat bacteria is that of the predominant sausage-shaped bacteria.
Amelioration of oxidative stress by dandelion extract through CYP2E1 suppression against acute liver injury induced by carbon tetrachloride in sprague‐dawley rats

The protective effects of common dandelion leaf water extract (DLWE) were investigated by carbon tetrachloride (CCl4) induced hepatitis in Sprague‐Dawley rats. The animals were divided into five groups: normal control, DLWE control, CCl4 control, and two DLWE groups (0.5 and 2 g/kg bw). After 1 week of administering corresponding vehicle or DLWE, a single dose of CCl4 (50% CCl4/olive oil; 0.5 mL/kg bw) was administered 24 h before killing in order to produce acute liver injury. The DLWE treatment significantly decreased CCl4‐induced hepatic enzyme activities (AST, ALT and LDH) in a dose dependent manner. Also, the obstructed release of TG and cholesterol into the serum was repaired by DLWE administration. Hepatic lipid peroxidation was elevated while the GSH content and antioxidative enzyme activities were reduced in the liver as a result of CCl4 administration, which were counteracted by DLWE administration. Furthermore, the hepatocytotoxic effects of CCl4 were confirmed by significantly elevated Fas and TNF‐? mRNA expression levels, but DLWE down‐regulated these expressions to the levels of the normal control. Highly up‐regulated cytochrome P450 2E1 was also lowered significantly in the DLWE groups. These results indicate that DLWE has a protective effect against CCl4‐induced hepatic damage with at least part of its effect being attributable to the attenuation of oxidative stress and inflammatory processes resulting from cytochrome P450 activation by CCl4. Copyright © 2010 John Wiley & Sons, Ltd.
A retrospective chart review of the effects of modafinil on depression as monotherapy and as adjunctive therapy

Major depression is often refractory to antidepressants, and it is important to explore alternative medication treatments. Among the symptoms common with depression are energy loss/fatigue and anxiety. Modafinil has a novel mechanism of action and may have antidepressant properties. In a single outpatient clinic, data were systematically collected on all patients including those who began modafinil treatment for major depression. This clinician (C.P.) had used modafinil to treat major depression in patients who failed one or more adequate antidepressant treatments. To monitor changes during treatment, charting had included four rating scales: the Beck Depression Inventory, the Zung Self‐Rating Depression Scale, and the Hamilton Depression and Hamilton Anxiety Rating Scales. A follow‐up chart review identified 45 patients whose major depression was treated with modafinil over a 9‐month period. The mean dose of modafinil was 184.3±100.0 mg/day (range=50–450 mg/day). For these 45 patients, all four rating scales showed significant improvement following 2 weeks and following 3 months of modafinil treatment. Fifteen of these patients were on modafinil monotherapy, and the remaining 30 on modafinil as an augmenting agent. For both subgroups, all three depression rating scales showed a significant improvement following 2 weeks and 3 months of modafinil treatment. This chart review provides preliminary evidence that modafinil treatment may be beneficial to those with major depression, even when unresponsive to other treatments. Depression and Anxiety 21:149–153, 2005. © 2005 Wiley‐Liss, Inc.