Miracle-dz/UniFAR-FTUs huggingface dataset:
Escherichia coli Open Reading Frame 696 Is idi, a Nonessential Gene Encoding Isopentenyl Diphosphate Isomerase

ABSTRACT Isopentenyl diphosphate isomerase catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In eukaryotes, archaebacteria, and some bacteria, IPP is synthesized from acetyl coenzyme A by the mevalonate pathway. The subsequent isomerization of IPP to DMAPP activates the five-carbon isoprene unit for subsequent prenyl transfer reactions. In Escherichia coli, the isoprene unit is synthesized from pyruvate and glyceraldehyde-3-phosphate by the recently discovered nonmevalonate pathway. An open reading frame (ORF696) encoding a putative IPP isomerase was identified in the E. coli chromosome at 65.3 min. ORF696 was cloned into an expression vector; the 20.5 kDa recombinant protein was purified in three steps, and its identity as an IPP isomerase was established biochemically. The gene for IPP isomerase, idi, is not clustered with other known genes for enzymes in the isoprenoid pathway. E. coli FH12 was constructed by disruption of the chromosomal idi gene with the aminoglycoside 3′-phosphotransferase gene and complemented by the wild-type idi gene on plasmid pFMH33 with a temperature-sensitive origin of replication. FH12/pFMH33 was able to grow at the restrictive temperature of 44°C and FH12 lacking the plasmid grew on minimal medium, thereby establishing thatidi is a nonessential gene. Although theVmax of the bacterial protein was 20-fold lower than that of its yeast counterpart, the catalytic efficiencies of the two enzymes were similar through a counterbalance inKms. The E. coli protein requires Mg2+ or Mn2+ for activity. The enzyme contains conserved cysteine and glutamate active-site residues found in other IPP isomerases.
Impact of Recent Fracture on Health‐Related Quality of Life in Postmenopausal Women

The effect of fractures other than hip and spine on HRQoL in younger and older women has not been extensively studied. In a cohort of 86,128 postmenopausal women, we found the impact of recent osteoporosis‐related fractures on HRQoL to be similar between women <65 compared with those ≥65 years of age. The impact of spine, hip, or rib fractures was greater than that of wrist fractures in both age groups.
The Legacy of Colonial Language Policies and Their Impact on Student Learning: Evidence from an Experimental Program in Cameroon

The relative educational returns on colonial versus indigenous language instruction in sub-Saharan countries have yet to be decisively estimated. To address this unanswered question, this paper provides an impact assessment of an experiment in Cameroon in which the first 3 years of schooling were conducted in a local language instead of in English. Test results in examinations in both English and math reveal that treated students exhibit gains of 1.1–1.4 of a standard deviation in grades 1 and 3 compared with the control students. It also increases the probability of being present in grades 3 and 5 by 22 and 14 percentage points, respectively. However, by the end of fifth grade, 2 years after reverting to the English stream, treated students still exhibit gains of 0.40–0.60 of a standard deviation, although the absolute scores for both groups are low enough to suggest limited learning is taking place.
Image Contour Extraction Based on CNN and Active Contour Model

A CNN is a dynamic nonlinear system with the local connectivity of cells and easy to be translated into a VLSI implementation. CNNs are very suitable for modeling the physical process of energy propagation since CNNs conserve the physical properties of a continuous structure. For the contour extraction, this paper proposes a method for establishing the evolution model of active contour by CNN technique. Further, the relationship between CNNs and the minimization for active contour model is investigated and the derivation of the CNN implementations for converting the active contour model to CNN templates is performed in order to improve the computing efficiency. Experimental results are given to demonstrate the feasibility of the proposed method in extracting contour from the blurred edge and highnoise images.
Exchange Rates and Stock Prices in Ghana

Using daily data spanning from January 2, 1998 to December 20, 2011, the study investigated the cointegration and the Granger causality relationships between exchange rates and stock prices in Ghana. Augmented Dickey-Fuller test was used to test for unit root process in the data series and the results show that both variables are integrated at order one, I (1). The Engle-Granger (1987) two-step cointegration test was used to test for cointegration between the two variables. The results show that there is no cointegration relationship between the two. Also, a structural break in the relationship between the two variables after the redenomination of the Ghana’s currency (Cedi) on July 3, 2007 was noticed. In effect, VAR between the stock price and exchange rate returns for pre-redenomination and post-redenomination sub-sample periods and consequently test for Granger causality. Unidirectional causality from exchange rates to stock prices before the redenomination but no causality between the two after the redenomination of the cedi.
Reorganization of cholangiocyte membrane domains represents an early event in rat liver ischemia

Cholangiocytes contribute significantly to bile formation through the vectorial secretion of water and electrolytes and are a focal site of injury in a number of diseases including liver ischemia and post‐transplantation liver failure. Using ischemia in intact liver and adenosine triphosphate (ATP) depletion in cultured cells to model cholangiocyte injury, these studies examined the effects of metabolic inhibition on cholangiocyte viability and structure. During 120 minutes of ischemia or ATP depletion, cell viability and tight junctional integrity in cholangiocytes were maintained. However, both the in vivo and in vitro models displayed striking alterations in the secondary structure of the plasma membrane. After 120 minutes, the basolateral (BL) interdigitations were diminished and the apical (Ap) microvilli were significantly decreased in number. The BL and Ap membrane surface areas decreased by 42 ± 8% and 63 ± 2%, respectively. Despite these changes, F‐actin remained predominantly localized to the membrane domains. In contrast, in a time course that paralleled the loss of microvilli, the actin‐membrane linking protein ezrin progressively dissociated from the cytoskeleton. These studies indicate that cholangiocyte ATP depletion induces characteristic, domain‐specific changes in the plasma membrane and implicate alterations in the membrane‐cytoskeletal interactions in the initiation of the changes. Pending the re‐establishment of the differentiated domains, the loss of specific secondary structures may contribute to impaired vectorial bile duct secretion and postischemic cholestasis.
Controller design for a 3-DOF helicopter using multiple models with second level adaptation

In this article, an adaptive model following control of a nonlinear multi-input multi-output (MIMO) coupled system with unknown parameters is considered. The decoupling matrix of the system is assumed to be singular, so that the system can not be decoupled by static state feedback. A dynamic state feedback with nonlinear structure algorithm is applied to design the controller. An observer is used to estimate the unknown parameters of the system. A multiple model with second level adaptation is introduced for the nonlinear MIMO coupled system. A 3-DOF (degree-of-freedom) helicopter model is simulated to validate the theoretical establishments. The advantage of using second level adaptation is established by conducting simulation studies.
Cloning and characterization of the Escherichia coli K-12 rfa-2 (rfaC) gene, a gene required for lipopolysaccharide inner core synthesis

A genetically defined mutation, designated rfa-2, results in altered lipopolysaccharide (LPS) biosynthesis. rfa-2 mutants produce a core-defective LPS that contains lipid A and a single sugar moiety, 2-keto-3-deoxyoctulosonic acid, in the LPS core region. Such LPS core-defective or deep-rough (R) mutant structures were previously designated chemotype Re. Phenotypically, rfa-2 mutants exhibit increased permeability to a number of hydrophilic and hydrophobic agents. By restriction analyses and complementation studies, we clearly defined the rfa-2 gene on a 1,056-bp AluI-DraI fragment. The rfa-2 gene and the flanking rfa locus regions were completely sequenced. Additionally, the location of the rfa-2 gene on the physical map of the Escherichia coli chromosome was determined. The rfa-2 gene encodes a 36,000-dalton polypeptide in an in vivo expression system. N-terminal analysis of the purified rfa-2 gene product confirmed the first 24 amino acid residues as deduced from the nucleotide sequence of the rfa-2 gene coding region. By interspecies complementation, a Salmonella typhimurium rfaC mutant (LPS chemotype Re) is transformed with the E. coli rfa-2+ gene, and the transformant is characterized by wild-type sensitivity to novobiocin (i.e., uninhibited growth at 600 micrograms of novobiocin per ml) and restoration of the ability to synthesize wild-type LPS structures. On the basis of the identity and significant similarity of the rfa-2 gene sequence and its product to the recently defined (D. M. Sirisena, K. A. Brozek, P. R. MacLachlan, K. E. Sanderson, and C. R. H. Raetz, J. Biol. Chem. 267:18874-18884, 1992), the S. typhimurium rfaC gene sequence and its product (heptosyltransferase 1), the E. coli K-12 rfa-2 locus will be designated rfaC.
Domestic and Export Performances of French Firms

The French trade balance deteriorated almost continuously from the late 1990s to the early 2010s. At the macroeconomic level, French export market share deteriorated while domestic sales kept pace with domestic demand. Does this assessment apply to individual firms? Using microlevel data for French industrial firms over the period 2002–12, we explore the link between domestic and export sales. We show that export and domestic sales have a tendency, albeit slight, to move in opposite directions. This may be due to factors such as deliberate strategies to target a specific market or the presence of production constraints. Addressing the resulting endogeneity issue, our analysis shows that a positive demand shock in the domestic market also leads to an increase in exports. In particular, a 10% increase in domestic demand leads to a 4% increase in exports. This complementarity between markets seems to be driven by small firms and could reflect the existence of liquidity constraints. Increased sales in one market could lessen these constraints by facilitating funding for company development in the export market.
The extraction of aggregates in Serbia, 1973-2015, a statistical exploration

We contribute to the fields of mineral economics, environmental and economic history in two respects: first, we construct a novel time series data set for the levels of aggregates extraction in Serbia between 1973 and 2015; the second, we estimate a change point ordinary least squares regression to model the dynamics of aggregates extraction in the aforementioned period. Our cliometric estimates are in great accordance with the major business cycle facts of the Serbian economy in the last 40 years. The most important policy implication of our results pertains to the potential slowdown of aggregates extraction from the onset of the Great Recession.
Lexical Selectivity in Danish Toddlers with Cleft Palate

Objective To study if Danish children with cleft palate display lexical selectivity in their early lexicon at 18 months of age. Design A cross-sectional study. Participants Thirty-four children with unilateral cleft lip and palate and 35 children without cleft palate, matched for gender and age. Methods All participants were video recorded at 18 months of age during play interaction with a parent. The video recordings were transcribed according to the International Phonetic Alphabet and an individual consonant inventory was established for each participant. The video recordings were also analyzed with respect to word productions, establishing an observed productive vocabulary size for each participant. Results At 18 months of age Danish children with cleft palate showed marked lexical selectivity in their early words. The distribution of consonant classes observed at 11 months of age in a previous study of the children with cleft palate was almost perfectly reflected in their early lexicon at 18 months. The early lexicon of children with cleft palate differed from the early lexicon of their noncleft peers. Conclusions and Implications Danish toddlers with cleft palate display lexical selectivity in the early lexicon as it has been described for English-speaking toddlers with and without cleft palate, even though some qualitative differences were found.
The Effects on Anchoring of Increasing Quantities of Disconfirming Evidence

Anchoring has been shown to influence judgements in a wide variety of contexts, often in a dysfunctional manner (particularly when anchors are deemed unreliable). Identifying methods for mitigating the effects of anchors is important. Our experimental study utilises three abstract settings and arbitrary anchor values. We find strong anchoring effects in initial judgements. Providing disconfirming evidence of moderate helpfulness does, however, reduce the anchoring effects. Specifically, providing one or two items of disconfirming information is shown to have significant incremental benefits in reducing or even eliminating anchoring effects. However, surprisingly, providing three items of disconfirming information, in our setting, did not further reduce anchoring, suggesting some diminishing effect of additional evidence. This is consistent with prior research suggesting that individuals adjust until they are 'close enough', and then stop considering additional information. Our results have implications for a wide variety of judgement contexts, and the results are encouraging in suggesting that a relatively small quantity of disconfirming evidence could be sufficient for overcoming anchoring.
Sexual conflict is not counterbalanced by good genes in the laboratory Drosophila melanogaster model system

Sexual conflict theory is based on the observation that females of many species are harmed through their interactions with males. Direct harm to females, however, can potentially be counterbalanced by indirect genetic benefits, where females make up for a reduction in offspring quantity by an increase in offspring quality through a generic increase in offspring fitness (good genes) and/or one restricted to the context of sexual selection (sexy sons). Here, we quantify the magnitude of the good genes mechanism of indirect benefits in a laboratory‐adapted population of Drosophila melanogaster. We find that despite high‐standing genetic variance for fitness, females gain at most only a modest benefit through the good genes form of indirect benefits – far too little to counterbalance the direct cost of male‐induced harm.
C2-DLM: Cache coherence aware dual link mesh for on-chip interconnect

Throughput-sensitive server workloads are expected to handle voluminous independent and concurrent transactions that require careful designing of an on chip interconnect. State of the art applications take in a very high and even unbounded working sets with concurrent data. It demands for suitable architectural changes for on chip interconnect to maintain the performance of concurrent applications. In this paper, we have proposed a novel dual link mesh on chip interconnect to classify cache traffic for cache coherence MESI directory protocol.
Essays on fitting factor models for asset returns

Essays on Fitting Factor Models for Asset Returns Sangeetha Srinivasan Chair of the Supervisory Committee: Professor Eric Zivot Department of Economics Factor models are used to describe the fundamental drivers of financial asset returns. There are 3 types: time-series factor, statistical factor and fundamental factor models. While factor models have existed for almost 60 years, industry-wide adoption with factor-based investing has surged in the last decade. This dissertation is centered on factorAnalytics, an open source R package codeveloped with other UW students and faculty members, that demystifies the industry black-box models, making model fitting tools readily available for any interested academic or practitioner. Chapter 1 compares the characteristics of the three types of models in terms of model specification, estimation, interpretation and various in-sample and out-of-sample performance metrics using S&P 500 stock returns. Like Connor (1995), we find that the fundamental factor model outperforms the time-series and statistical factor models since it makes use of additional information on asset-specific characteristics. Moreover, we find that adding statistical factor(s) extracted from the residuals of time-series or fundamental factor models, or, fitting fundamental factors to the residuals of a time-series factor model, to create hybrid models, further improves performance. Investment management firms need to understand peer positioning for a variety of reasons, including risk management. Factor models provide a framework to estimate peer exposures, especially useful when holdings-based information is lacking. Chapter 2 presents a multi-asset time-series factor model constructed from long-short portfolios of asset class index returns, applied to peer-average returns from the Morningstar U.S. fund allocation categories. We show that factors are better than asset classes for assessing unknown exposures and decomposing risk in multi-asset portfolios. Furthermore, there is an opportunity to create more efficient, better riskdiversified portfolios using factors when making allocation decisions. We use the multi-factor model to construct equal-asset-risk and equal-factor-risk portfolios and compare them to the equal-weighted and minimum-variance portfolios. We also show that a zero-investment equalfactor-risk portfolio sleeve helps bridge the gap between pure risk parity and traditional portfolios, enhancing Sharpe ratio across all risk categories. Chapters 3-5 contain vignettes for each type of factor model that describe and demonstrate model fitting, factor risk (volatility, value-at-risk and expected shortfall) decomposition, and related S3 generic methods.
‘They Light The Christmas Tree in Our Town’

Sport occupies a prominent space in the public lives and private identities of US adolescents. Using the retrospective reflections of college students, this analysis explores two questions about sport-related identities during high school: Are ‘athletes’ and ‘jocks’ distinctly separate identities? Are these identities explicitly gendered? In four gender-segregated focus groups conducted in early 2005, 32 student-athletes from two upstate New York colleges discussed their high school experiences of sport, status, gender, and identity. Three primary themes developed with regard to differences between the ‘jock’ and ‘athlete’ archetypes: academic focus, teamwork, and cockiness/ aggression. Examining the intersection of gender, high-status/high-profile sport, and identity in both popular cultural imagery and the personal experiences of the focus group discussants provided support for the thesis of a ‘toxic jock’ phenomenon.
Effects of hypervolemia and hypertension on regional cerebral blood flow, intracranial pressure, and brain tissue oxygenation after subarachnoid hemorrhage*

Objective:Hypertensive, hypervolemic, hemodilution therapy (triple-H therapy) is a generally accepted treatment for cerebral vasospasm after subarachnoid hemorrhage. However, the particular role of the three components of triple-H therapy remains controversial. The aim of the study was to investigate the influence of the three arms of triple-H therapy on regional cerebral blood flow and brain tissue oxygenation. Design:Animal research and clinical intervention study. Setting:Surgical intensive care unit of a university hospital. Subjects and Patients:Experiments were carried out in five healthy pigs, followed by a clinical investigation of ten patients with subarachnoid hemorrhage. Interventions:First, we investigated the effect of the three components of triple-H therapy under physiologic conditions in an experimental pig model. In the next step we applied the same study protocol to patients following aneurysmal subarachnoid hemorrhage. Mean arterial pressure, intracranial pressure, cerebral perfusion pressure, cardiac output, regional cerebral blood flow, and brain tissue oxygenation were continuously recorded. Intrathoracic blood volume and central venous pressure were measured intermittently. Vasopressors and/or colloids and crystalloids were administered to stepwise establish the three components of triple-H therapy. Measurements and Main Results:In the animals, neither induced hypertension nor hypervolemia had an effect on intracranial pressure, brain tissue oxygenation, or regional cerebral blood flow. In the patient population, induction of hypertension (mean arterial pressure 143 ± 10 mm Hg) resulted in a significant (p < .05) increase of regional cerebral blood flow and brain tissue oxygenation at all observation time points. In contrast, hypervolemia/hemodilution (intrathoracic blood volume index 1123 ± 152 mL/m2) induced only a slight increase of regional cerebral blood flow while brain tissue oxygenation did not improve. Finally, triple-H therapy failed to improve regional cerebral blood flow more than hypertension alone and was characterized by the drawback that the hypervolemia/hemodilution component reversed the effect of induced hypertension on brain tissue oxygenation. Conclusions:Vasopressor-induced elevation of mean arterial pressure caused a significant increase of regional cerebral blood flow and brain tissue oxygenation in all patients with subarachnoid hemorrhage. Volume expansion resulted in a slight effect on regional cerebral blood flow only but reversed the effect on brain tissue oxygenation. In view of the questionable benefit of hypervolemia on regional cerebral blood flow and the negative consequences on brain tissue oxygenation together with the increased risk of complications, hypervolemic therapy as a part of triple-H therapy should be applied with utmost caution.
Flow cytometric analysis of SOX11: a new diagnostic method for distinguishing B-cell chronic lymphocytic leukemia/small lymphocytic lymphoma from mantle cell lymphoma

Abstract The differential diagnosis between mantle cell lymphoma (MCL) and B-cell chronic lymphocytic leukemia/small lymphocytic lymphoma (B-CLL/SLL) is essential, since MCL usually has a more aggressive clinical course. By flow cytometry both MCL and B-CLL are CD19, CD20 and usually CD5 positive. However, ambiguities in other immune phenotypic markers of these lymphoma entities sometimes complicate the flow cytometric differential diagnosis. We here demonstrate that the transcription factor SOX11, which is highly up-regulated in most MCL, can be analyzed by flow cytometry. SOX11 protein could be consistently detected in ex vivo isolated MCL but not in B-CLL/SLL. Flow cytometry also enabled protein quantification, and SOX11 protein levels correlated with mRNA expression. We suggest that implementing detection of SOX11 in diagnostic flow cytometry would be beneficial for accurate and reliable diagnosis of MCL, especially for distinguishing cases of MCL and B-CLL/SLL with aberrant immune phenotypes, and for cases of rare cyclin D1 negative MCL.