Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal Structures of 4-α-Glucanotransferase from Thermococcus litoralis and Its Complex with an Inhibitor*

Thermococcus litoralis 4-α-glucanotransferase (TLGT) belongs to glucoside hydrolase family 57 and catalyzes the disproportionation of amylose and the formation of large cyclic α-1,4-glucan (cycloamylose) from linear amylose. We determined the crystal structure of TLGT with and without an inhibitor, acarbose. TLGT is composed of two domains: an N-terminal domain (domain I), which contains a (β/α)7 barrel fold, and a C-terminal domain (domain II), which has a twisted β-sandwich fold. In the structure of TLGT complexed with acarbose, the inhibitor was bound at the cleft within domain I, indicating that domain I is a catalytic domain of TLGT. The acarbose-bound structure also clarified that Glu123 and Asp214 were the catalytic nucleophile and acid/base catalyst, respectively, and revealed the residues involved in substrate binding. It seemed that TLGT produces large cyclic glucans by preventing the production of small cyclic glucans by steric hindrance, which is achieved by three lids protruding into the active site cleft, as well as an extended active site cleft. Interestingly, domain I of TLGT shares some structural features with the catalytic domain of Golgi α-mannosidase from Drosophila melanogaster, which belongs to glucoside hydrolase family 38. Furthermore, the catalytic residue of the two enzymes is located in the same position. These observations suggest that families 57 and 38 evolved from a common ancestor.
Heat shock proteins and cancer: intracellular chaperones or extracellular signalling ligands?

Heat shock proteins (HSPs) are found at elevated concentrations in tumour cells, and this increase reflects the proteotoxic stress experienced by the cells due to expanding levels of the mutated oncoproteins that drive tumorigenesis. The protection of oncogenic proteins by HSPs offers a window of vulnerability in tumour metabolism that has been exploited using Hsp90-targeting drugs. Such compounds have been shown to cause inhibition and degradation of a wide range of proteins essential for oncogenesis. Recently, Hsp90 has also been shown to be secreted by tumour cells and to interact in autocrine or paracrine manners with the surfaces of adjacent cells, leading to increased growth and metastasis. Future studies will address a number of key questions associated with these findings, including the relative importance of intracellular versus extracellular HSPs in tumorigenesis, as well as overcoming potential problems with normal tissue toxicity associated with Hsp90 drugs. Targeting individual members of HSP families and inactivating extracellular HSPs may be desirable future approaches that offer increased selectivity in targeting HSPs in cancer. This article is part of the theme issue ‘Heat shock proteins as modulators and therapeutic targets of chronic disease: an integrated perspective’.
IgM and IgG but not cytokine secretion is restricted to the CD27+ B lymphocyte subset.

In a recent study we reported that CD27 is expressed on a subpopulation of human B lymphocytes and presented circumstantial phenotypic evidence that CD27 expression may be acquired late during B cell differentiation. Here we present functional data showing that, after in vitro stimulation, CD27+ but not CD27- B cells secrete large amounts of both IgM and IgG. Using double immunofluorescence staining of CD27 and IgD, three functionally different B cell subsets representing distinct stages of B cell differentiation can be isolated: 1) the CD27- IgD+ B cells, which do not secrete appreciable Ig; 2) the CD27+IgD+ B cells, which exclusively secrete IgM; and 3) the CD27+IgD- B cells, which comprise the IgG-producing cells. Furthermore, costimulation of CD27- B cells with low m.w. B cell growth factor, in the presence or in the absence of a CD40 mAb, does not induce these cells to become Ig-secreting cells. Although CD27- B cells hardly secrete Ig of any isotype in response to Staphylococcus aureus+IL-2, these cells proliferate vigorously and express the IL-2R alpha chain (CD25) under these stimulatory conditions. Furthermore, both CD27- and CD27+ B cells are capable of producing similar amounts of IL-6 and TNF-alpha. Taken together, these findings indicate that CD27 is a unique non-Ig surface marker discriminating naive from primed B lymphocytes. Furthermore, the capacity to proliferate and to secrete the B cell differentiation factors IL-6 and TNF-alpha already exists at an early B cell differentiation stage at which the cells lack CD27 expression and are not induced to produce Ig.
New Public Management and Administrative Reforms in Nigeria

ABSTRACT This study examines the Nigerian attempts to implement the New Public Management (NPM) reform. The paper aims at identifying the strand, the extent of progress made and the reason(s) for success/failure recorded. The author finds that the poor success story of the reform is as a result of the preference of the more attractive cost-saving neoliberal economic aspect to the more involving and demanding bureaucratic aspect, the inconsistencies in program implementation, and lack of strong political will common to adopting reform in developing countries. The article recommends that reforms require dealing with the critical challenges of institutionalization, inconsistency and legitimization.
"More than Just a Teacher”: Anticipatory Advocacy as Vision and Defense in Urban High-need Schools

Specialized teacher preparation programs are graduating teachers with commitments to advocacy. This expanded definition of teaching stands in opposition to traditional expectations for the role of teachers that have developed during the history of U.S. education into organizational and social frames that reinforce tradition and work against reform. These influences constitute forces of professional weathering that may wear down teachers’ visions and actions for their work. This multicase study focused on four graduates from an intensive twoyear teacher preparation program that included initial certification along with induction support in the second year of the program as they completed master’s degree requirements. The inquiry sought to understand how they envisioned their roles as teacher advocates and how they enacted and sustained their visions, resisting traditional teacher roles. Participants were graduates of the same cohort of the preparation program who were completing their second year of teaching in urban high-need schools and who had been nominated and confirmed as effective teachers of diverse students by faculty members of the university program and of local schools. Program materials were analyzed as background material to establish context. Primary data that were inductively and iteratively analyzed included extant course assignments, three individual interviews with each participant, three school-related observations, and three focus group interviews. Findings provide insight into the ways in which the teachers enacted a vision of anticipatory advocacy. Anticpatory advocacy includes intervening actions that are the result of a dual awareness of students’ immediate and future needs and have implications beyond boundaries of time and space in an effort to positively influence students’ lives in the immediate as well as distant future. The teachers, each of whom held beliefs that aligned with the culturally relevant foundations of the program prior to their selection, employed tools related to responsive classroom management, ambitious teaching strategies, and professional collaboration that they acquired and honed during their program. By working backward from the classrooms of effective teachers, the study links classroom practices with teacher preparation, providing direction for stakeholders concerned with the development and retention of high quality teachers for all children, especially in challenging school contexts. INDEX WORDS: Anticipatory advocacy, Visioning, Culturally relevant pedagogy, Urban education, Diverse students, Novice teachers, Teacher education, Classroom management, Ambitious teaching, Professional weathering “MORE THAN JUST A TEACHER”: ANTICIPATORY ADVOCACY AS VISION AND DEFENSE IN URBAN HIGH-NEED SCHOOLS by Kim Stevens Barker
High quality voice conversion based on ISODATA clustering algorithm

Two main challenges introduced in current voice conversion are the dependence on parallel training data and the trade-off between speaker similarity and speech quality. To tackle the latter problem, this paper proposes a novel conversion method based on Iterative Self-organizing DATA Analysis Techniques Algorithm (ISODATA) clustering algorithm. Specially, we use ISODATA during the training of Gaussian mixture model, the optimized mixture number can guarantee the validity and accuracy of the GMM model, which can acquire speaker's identity effectively related to speaker similarity between original target speech and converted speech, Next, we combine improved GMM and bilinear frequency warping for the conversion stage, which can get a good balance between speaker similarity and speech quality. Theory analysis and experimental results demonstrate that the proposed algorithm can achieve higher quality and similarity compared with other two methods.
A 220 MHz low phase noise Colpitts oscillator

This paper presents the design of a VCO using Colpitts topology. The VCO is designed to work at 220 MHz as part of the Frequency Generating Unit (FGU). The circuit has been realized by discrete level circuits. The frequency range is between 217 MHz and 222 Mhz. The low phase noise of −122 dBc/Hz at 20 kHz offset frequency was achieved by the varactor tuned Colpitts oscillator. Both simulation and measurements demonstrate the low noise performance.
The Probiotic Bacterium Lactobacillus casei Induces Activation of the Gut Mucosal Immune System through Innate Immunity

ABSTRACT The mechanisms by which probiotic bacteria affect the immune system are unknown yet, but many of them are attributed to an increase in the innate or in the acquired immune response. To study the influence of the probiotic bacterium Lactobacillus casei in the expression of receptors involved in the innate immune response, this bacterium was orally administered to BALB/c mice. After, they were sacrificed; the small intestine and intestinal fluids were collected to measure secretory immunoglobulin A (IgA) specific for L. casei. Mononuclear cells from Peyer's patches were isolated to determine the CD-206 and TLR-2 receptors. In histological slices we determined the number of IgA+, CD4+, CD8+, and CD3+ cells and two cytokines (interleulin-5 [IL-5] and IL-6). CD-206 and TLR-2 increased with respect to the untreated control. We did not observe an increase in the T population or in the IL-5-positive cells. IgA+ cells and IL-6-producing cells increased after 7 days of L. casei administration. We did not find specific antibodies against L. casei. The main immune cells activated after oral L. casei administration were those of the innate immune response, with an increase in the specific markers of these cells (CD-206 and TLR-2), with no modification in the number of T cells.
Rhodopsin Phosphorylation Sites and Their Role in Arrestin Binding*

Rhodopsin, the rod cell photoreceptor, undergoes rapid desensitization upon exposure to light, resulting in uncoupling of the receptor from its G protein, transducin (Gt). Phosphorylation of serine and threonine residues located in the COOH terminus of rhodopsin is the first step in this process, followed by the binding of arrestin. In this study, a series of mutants was generated in which these COOH-terminal phosphorylation substrate sites were substituted with alanines. These mutants were expressed in HEK-293 cells and analyzed for their ability to be phosphorylated by rhodopsin kinase and to bind arrestin. The results demonstrate that rhodopsin kinase can efficiently phosphorylate other serine and threonine residues in the absence of the sites reported to be the preferred substrates for rhodopsin kinase. A correlation was observed between the level of rhodopsin phosphorylation and the amount of arrestin binding to these mutants. However, mutants T340A and S343A demonstrated a significant reduction in arrestin binding even though the level of phosphorylation was similar to that of wild-type rhodopsin. Substitution of Thr-340 and Ser-343 with glutamic acid residues (T340E and S343E, respectively) was not sufficient to promote the binding of arrestin in the absence of phosphorylation by rhodopsin kinase. When S343E was phosphorylated, its ability to bind arrestin was similar to that of wild-type rhodopsin. Surprisingly, arrestin binding to phosphorylated T340E did not increase to the level observed for wild-type rhodopsin. These results suggest that 2 amino acids, Thr-340 and Ser-343, play important but distinct roles in promoting the binding of arrestin to rhodopsin.
Hidden histories of gene flow in highland birds revealed with genomic markers

Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species‐rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well‐studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mtDNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these ‘hidden histories’ using genomic markers known as ultraconserved elements (UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation‐with‐bouts‐of‐gene‐flow will turn out to be a common mode of speciation.
Effect of cortisol levels on working memory performance in elderly subjects with Alzheimer's disease.

BACKGROUND Subjects with Alzheimer's disease (AD) have elevated cortisol levels as a result of hypothalamic-pituitary-adrenal (HPA) axis dysfunction. Acute administration of hydrocortisone has been associated with working memory (WM) performance in young adults. OBJECTIVE To investigate whether cortisol levels are associated with WM performance in subjects with AD. METHOD Eighty subjects were included, comprising 40 patients with mild AD and 40 healthy elderly controls. WM was assessed using the Digit Span Backward test (DSB). Saliva samples were collected to determine cortisol levels. RESULTS AD subjects had poorer performance on the DSB than controls (p=0.002) and also presented higher levels of cortisol than control group (p=0.04). No significant correlation was observed between the DSB and cortisol levels in both groups (r= -0.29). CONCLUSION In this study, elevated cortisol levels were not associated with poorer WM performance in patients with AD or in healthy elderly subjects.
Increasing rates of gastroenteritis hospital discharges in US adults and the contribution of norovirus, 1996-2007.

BACKGROUND Diarrhea remains an important cause of morbidity, but until the mid 1990s, hospital admissions for diarrhea in the US adult population were declining. We aimed to describe recent trends in gastroenteritis hospitalizations and to determine the contribution of norovirus. METHODS We analyzed all gastroenteritis-associated hospital discharges during 1996-2007 from a nationally representative data set of hospital inpatient stays. Annual rates of discharges by age were calculated. Time-series regression models were fitted using cause-specified discharges as explanatory variables; model residuals were analyzed to estimate norovirus- and rotavirus-associated discharges. We then calculated the annual hospital charges for norovirus-associated discharges. RESULTS Sixty-nine percent of all gastroenteritis discharges were cause-unspecified and rates increased by ≥ 50% in all adult and elderly age groups (≥ 18 years of age) from 1996 through 2007. We estimate an annual mean of 71,000 norovirus-associated hospitalizations, costing $493 million per year, with surges to nearly 110,000 hospitalizations per year in epidemic seasons. We also estimate 24,000 rotavirus hospitalizations annually among individuals aged ≥ 5 years. CONCLUSIONS Gastroenteritis hospitalizations are increasing, and we estimate that norovirus is the cause of 10% of cause-unspecified and 7% of all-cause gastroenteritis discharges. Norovirus should be routinely considered as a cause of gastroenteritis hospitalization.
Crystal Structure of Calmodulin Binding Domain of Orai1 in Complex with Ca2+•Calmodulin Displays a Unique Binding Mode*

Background: Calmodulin (CaM) binds the calmodulin binding domain (CMBD) of Orai1 causing Ca2+·CaM-dependent inhibition (CDI). Results: Orai1-CMBD binds the C-lobe of CaM in crystal, whereas in solution Orai1-CMBD interacts with both N- and C-lobes of CaM. Conclusion: One CaM, in an extended conformation, binds to two Orai1-CMBDs. Significance: This expands our knowledge of the interaction of CaM with its targets, and provides important information for understanding CDI. Orai1 is a plasma membrane protein that in its tetrameric form is responsible for calcium influx from the extracellular environment into the cytosol in response to interaction with the Ca2+-depletion sensor STIM1. This is followed by a fast Ca2+·calmodulin (CaM)-dependent inhibition, resulting from CaM binding to an Orai1 region called the calmodulin binding domain (CMBD). The interaction between Orai1 and CaM at the atomic level remains unknown. Here, we report the crystal structure of a CaM·Orai1-CMBD complex showing one CMBD bound to the C-terminal lobe of CaM, differing from other CaM-target protein complexes, in which both N- and C-terminal lobes of CaM (CaM-N and CaM-C) are involved in target binding. Orai1-CMBD binds CaM-C mainly through hydrophobic interactions, primarily involving residue Trp76 of Orai1-CMBD, which interacts with the hydrophobic pocket of CaM-C. However, NMR data, isothermal titration calorimetry data, and pulldown assays indicated that CaM-N and CaM-C both can bind Orai1-CMBD, with CaM-N having ∼4 times weaker affinity than CaM-C. Pulldown assays of a Orai1-CMBD(W76E) mutant, gel filtration chromatography data, and NOE signals indicated that CaM-N and CaM-C can each bind one Orai1-CMBD. Thus our studies support an unusual, extended 1:2 binding mode of CaM to Orai1-CMBDs, and quantify the affinity of Orai1 for CaM. We propose a two-step mechanism for CaM-dependent Orai1 inactivation initiated by binding of the C-lobe of CaM to the CMBD of one Orai1 followed by the binding of the N-lobe of CaM to the CMBD of a neighboring Orai1.
Clinical vs. Arthrographic Diagnosis of TMJ Internal Derangement

Internal derangements of the temporomandibular joint (TMJ) have gained increased recognition as a potential source of pain and dysfunction of the masticatory system. The objective of this study was to evaluate the reliability of clinicians in predicting an arthrographic diagnosis of articular disc position in a typical patient population presenting for TMJ arthrographic evaluation. Two clinicians utilized a brief history, clinical examination (including evaluation of mandibular movement and TMJ auscultation), and tomographic TMJ imaging in evaluating 60 patients. The radiologist subsequently performed the arthrographic procedures on 102 TMJs (18 unilateral and 42 bilateral). Diagnostic agreement was determined for all possible diagnostic categories including: normal disc position, TMJ internal derangement with reduction, TMJ internal derangement without reduction/acute, TMJ internal derangement without reductionlchronic, and osteoarthrosis. The significance of the diagnostic agreement between the clinicians and arthrography was evaluated with a Kappa Statistical Test, which showed good reliability. For epidemiological studies, it was concluded that clinical and tomographic evaluation would provide sufficient reliability for determination of the presence and stage of TMJ internal derangement. However, in a specific clinical situation, a difficult diagnostic problem may require the use of arthrography, depending on the impact of the diagnosis on subsequent treatment decisions.
[Effects of Kupffer cells stimulated by triglyceride and very low-density lipoprotein on proliferation of rat hepatic stellate cells].

OBJECTIVE To study the effects of Kupffer cell-conditioned medium (KCCM) derived from triglyceride and very low-density lipoprotein (VLDL) treatment on proliferation of rat hepatic stellate cells (HSC). METHODS HSC and Kupffer cells were isolated from liver of Wistar rats by in situ perfusion with pronase and collagenase and density gradient centrifugation with Nycodenz and then cultured. KCCM was prepared and MTT colorimetric assay was used to detect HSC proliferation. RESULTS HSC and Kupffer cells were isolated successfully with high purity. 12.5 mg/L of triglyceride and 25 - 100 mg/L of VLDL promoted HSC proliferation (P < 0.05 or 0.01); KCCM + triglyceride and KCCM + VLDL might promote HSC proliferation as compared with a control group (P < 0.01). There was no significant difference between KCCM + triglyceride and KCCM + VLDL (P > 0.05). CONCLUSION The technique for isolation of HSC and Kupffer cells described here is simple and reliable. Triglyceride, VLDL and KCCM stimulated by them may promote HSC proliferation and be associated with fatty liver and hepatic fibrogenesis.
Role of Laser-Induced IR Drops in the Occurrence of Faults: Assessment and Simulation

Laser fault injection attacks induce transient faults into ICs by locally generating transient currents capable of temporarily flipping the outputs of logic gates. Laser fault injection may be anticipated or studied by using simulation tools at different abstraction levels: physical, electrical or logical. At the electrical level, the general laser-fault injection model is based on the addition of current sources to the various sensitive nodes of CMOS transistors. This type of electrical model does not take into account the large transient current components also induced between VDD and GND as a result of laser illumination. Such current components have no direct effect on the logic gate output nodes. Still, they provoke a significant IR-drop that may, in turn, contribute to the fault injection process. This paper describes our research on the assessment of this contribution. It introduces an upgraded electrical model taking the laser-induced IR-drop into account. It also proposes a methodology that allows the model’s use to simulate laser-induced faults at electrical level in large-scale circuits. On the basis of simulations with a case-study circuit, we found that, depending on the parameters of the laser pulse, the number of injected faults may be underestimated by a factor as large as 48 if the laser-induced IR-drop is ignored. This may lead to incorrect estimations of the fault injection threshold, which is especially relevant for the design of countermeasure techniques for secure integrated systems.