Miracle-dz/UniFAR-FTUs huggingface dataset:
A Comparison of Permutation and Bootstrap Tests

This paper compares the permutation and boo strap tests in the setting of a two sample testing of the equality of sample mean. Since Romano[4], Bradley and Tibshirani[2] already showed that the tests yield similar results in large sample hypothesis testings, but few, if any, literature investigated in the small sample cases, we will compare the permutation and bootstrap tests in the situation of a testing of the two sample mean in relatively small samples. For this paper, these samples will have equal size and variance. Specifically, we will investigate the relative value of the Type I Error rates and Type II Error rates of the permutation and bootstrap tests, and will use simulation results to investigate the required sample size for the tests to show similar results. We will also provide simulation results to visually understand the results proven by Romano, Bradley and Tibshirani of the large sample testing.
Assessment of the prevalence of the 985A>G MCAD mutation in the French‐Canadian population using allele‐specific PCR

Inherited deficiency of medium‐chain acyl‐CoA dehydrogenase (MCAD) is a severe, sometimes fatal disorder. A single mutation in the MCAD gene, 985A>G, is involved in approximately 90% of cases. To evaluate the relevance of implementing a systematic population‐based screening program in the province of Quebec using a biochemical test, we measured the prevalence of this mutation in a set of anonymous newborn samples from the Quebec City area, a region where the majority of its inhabitants are French‐Canadians. An allele‐specific polymerase chain reaction assay was designed and used to detect the mutation in 7143 DNA samples obtained from consecutive anonymous newborns. Pools of eight DNA samples were genotyped in parallel for the same mutation to validate this pooling strategy. The allelic frequency of the MCAD 985A>G mutation was found to be 0.71% and the carrier frequency 1:71 (95% confidence interval 1:55 to 1:98). This estimate predicts a homozygous frequency of 1:19,837. Ninety‐nine heterozygous carriers and one homozygous individual were identified out of 7143 samples. There was 100% concordance between the individual and pooled analyses, and the pooling strategy reduced the total genotyping costs by approximately 70%. The carrier frequency estimated for this population is similar to other northwestern European populations and would support implementation of systematic newborn screening (such as tandem mass spectrometry screening) for this disease. Pooling DNA samples followed by genotyping appears to be cost‐effective for estimating prevalence of rare mutations.
Expression of the Apoptosis‐Effector Gene, Bax, Is Up‐Regulated in Vulnerable Hippocampal CA1 Neurons Following Global Ischemia

Abstract: The observation that delayed death of CA1 neurons after global ischemia is inhibited by protein synthesis inhibitors suggests that the delayed death of these neurons is an active process that requires new gene expression. Delayed death in CA1 has some of the characteristics of apoptotic death; however, candidate proapoptotic proteins have not been identified in the CA1 after ischemia. We studied the expression of Bax protein and mRNA, a member of the bcl‐2 family that is an effector of apoptotic cell death, after global ischemia in the four‐vessel global ischemia model in the rat and compared these results with the expression of the antiapoptotic gene bcl‐2. Bax mRNA and protein are both expressed in CA1 before delayed death, whereas bcl‐2 protein is not expressed. Bcl‐2 protein expression, but not that of Bax, is increased in CA3, a region that is ischemic but less susceptible to ischemic injury. In the dentate gyrus, both Bax and bcl‐2 proteins are expressed. The selective expression of Bax in CA1 supports the hypothesis that Bax could contribute to delayed neuronal death in these vulnerable neurons by an independent mechanism or by forming heterodimers with gene family members other than bcl‐2.
The micropatterning of layers of colloidal quantum dots with inorganic ligands using selective wet etching

The micropatterning of layers of colloidal quantum dots (QDs) stabilized by inorganic ligands is demonstrated using PbS core and CdSe/CdS core/shell QDs. A layer-by-layer approach is used to assemble the QD films, where each cycle involves the deposition of a QD layer by dip-coating, and the replacement of the native organic ligands by inorganic moieties, such as OH− and S2−, followed by a thorough cleaning of the resulting film. This results in a smooth and crack-free QD film on which a photoresist can be spun. The micropatterns are defined by a positive photoresist, followed by the removal of uncovered QDs by selective wet etching with an HCl/H3PO4 mixture. The resulting patterns can have submicron feature dimensions, limited by the resolution of the lithographic process, and can be formed on planar and 3D substrates. It is shown that the photolithography and wet etching steps have little effect on the photoluminescence quantum yield of CdSe/CdS QDs. Compared with the unpatterned CdSe/CdS QD film, only a 10% degradation in the quantum yield is observed. These results demonstrate the feasibility of the proposed micropatterning method to implement the large-scale device integration of colloidal quantum dots.
Design and Experimental Development of a Pneumatic Stiffness Adjustable Foot System for Biped Robots Adaptable to Bumps on the Ground

Walking on rough terrains still remains a challenge that needs to be addressed for biped robots because the unevenness on the ground can easily disrupt the walking stability. This paper proposes a novel foot system with passively adjustable stiffness for biped robots which is adaptable to small-sized bumps on the ground. The robotic foot is developed by attaching eight pneumatic variable stiffness units to the sole separately and symmetrically. Each variable stiffness unit mainly consists of a pneumatic bladder and a mechanical reversing valve. When walking on rough ground, the pneumatic bladders in contact with bumps are compressed, and the corresponding reversing valves are triggered to expel out the air, enabling the pneumatic bladders to adapt to the bumps with low stiffness; while the other pneumatic bladders remain rigid and maintain stable contact with the ground, providing support to the biped robot. The performances of the proposed foot system, including the variable stiffness mechanism, the adaptability on the bumps of different heights, and the application on a biped robot prototype are demonstrated by various experiments.
The market segmentation in Malaysia by using psychographic dimensions

The rapidly changing market place environment has resulted in a majority of consumers at both national and international levels feeling confused and facing difficulties in making decisions. Among the contributing factors towards the phenomena are over-selection of products and services, sophisticated and complex products, innovative marketing communication, dumping of counterfeiting products and similarities in branding. In the same development, many scholars and researchers have long acknowledged the importance of knowing why customers choose a particular product and service and the factors that influence them to make the selection. In response to this competitive environment, scholars in the marketing field have introduced the concept of differentiation and market segmentation. The purpose of market segmentation is to identify the taxonomy of consumption patterns by dividing a market into several homogeneous sub-markets. By using this concept, marketers can formulate product strategies, or product positions, tailored specifically to the demands of these homogeneous sub-markets which are defined by predetermined segmentation variables (Chin, 2002, p.249) while companies can increase profitability by utilizing market segmentation. Furthermore, segmentation can also enhance marketing effectiveness and develop or maintain an organization’s ability to benefit from identifiable marketing opportunities (Weinstein, 1987 in Quinn, Hines and Bennison, 2007).
Neural stem cells, adult neurogenesis, and galectin‐1: From bench to bedside

Neural stem cells (NSCs) in the adult brain have been a consistent focus of biomedical research largely because of their potential clinical application. To fully exploit this potential, the molecular mechanisms that regulate NSCs must be clarified. Several lines of evidence show that a multifunctional protein, Galectin‐1, is expressed and has a functional role in a subset of adult NSCs. Researchers, including our group, have explored the physiological role of Galectin‐1 in NSCs and its application in the treatment of animal models of neurological disorders such as brain ischemia and spinal cord injury. Here, we summarize what is currently known regarding the role of Galectin‐1 in adult NSCs. Furthermore, we discuss current issues in researching the role of Galectin‐1 in adult NSCs under both physiological and pathological conditions. © 2012 Wiley Periodicals, Inc. Develop Neurobiol 72: 1059–1067, 2012
Prevalence and predictors of women's experience of psychological trauma during childbirth.

BACKGROUND The increased acceptance of the prevalence of trauma in human experience as well as its psychological consequences has led to revisions of diagnostic criteria for the disorder. The three purposes of this study were to examine the rates at which women experienced psychological trauma in childbirth, to explore possible causal factors, and to examine possible factors in the development of the disorder. METHODS One hundred and three women from childbirth education classes in the Atlanta metropolitan area completed a survey in late pregnancy and a follow-up interview approximately 4 weeks after the birth. RESULTS The childbirth experience was reported as traumatic by 34 percent of participants. Two women (1.9%) developed all the symptoms needed to diagnose posttraumatic stress disorder, and 31 women (30.1%) were partially symptomatic. Regression analysis showed that antecedent factors (e.g., history of sexual trauma and social support) and event characteristics (e.g., pain in first stage of labor, feelings of powerlessness, expectations, medical intervention, and interaction with medical personnel) were significant predictors of perceptions of the childbirth as traumatic. The pain experienced during the birth, levels of social support, self-efficacy, internal locus of control, trait anxiety, and coping were significant predictors of the development of posttraumatic stress disorder symptoms after the birth. CONCLUSIONS These findings suggest several intervention points for health care practitioners, including careful prenatal screening of past trauma history, social support, and expectations about the birth; improved communication and pain management during the birth; and opportunities to discuss the birth postpartum.
Identification of SARS-COV Spike Protein-Derived and HLA-A2-Restricted Human CTL Epitopes by Using a New Muramyl Dipeptide-Derivative Adjuvant

Severe acute respiratory syndrome (SARS) spread during the winter of 2003, and attempt have been made to develop vaccines against SARS corona virus (SARS-CoV). The present study provides a strategy to rapidly identify SARS-CoV-derived antigenic peptides recognized by HLA-A2-restricted cytotoxic T lymphocytes (CTLs). Forty-three candidate peptides having HLA-A2-binding motifs were selected in silico and HLA-A2/Db chimeric MHC class I-transgenic mice were immunized with these peptides and a new derivative of muramyl dipeptide that can induce upregulation of HLA-DR, CD80, CD86, and CD40 in human CD14+ antigen presenting cells, was administered as an adjuvant. Six HLA-A2-restricted mouse CTL epitopes were identified, including two new epitopes which have never been reported before. One of the novel peptides was naturally processed and successfully induced HLA-A2-restricted specific CTLs in both HLA transgenic mice and healthy donors. The method was useful, convenient and efficient for rapid identification of CTL epitopes derived from SARS-CoV proteins and will be possibly applicable for other pathogens to develop a peptide-based vaccine.
Complete nucleotide sequence of the new simian T-lymphotropic virus, STLV-PH969 from a Hamadryas baboon, and unusual features of its long terminal repeat

A third type of primate T-lymphotropic virus, PTLV-L, with STLV-PH969 as a prototype, has recently been isolated from an African baboon (Papio hamadryas). Classification of this virus has been based on partial sequence analysis of cDNA from a virus-producing cell line, PH969. We obtained the complete nucleotide sequence of this virus with a proviral genome of 8,916 bp. All major genes, homologous in all human T-cell lymphotropic virus (HTLV)-related viruses, and their corresponding mRNAs, including appropriate splicing, were identified. One additional nonhomologous open reading frame in the proximal pX region is accessible for translation through alternative splicing. Sequence comparison shows that STLV-PH969 is equidistantly related to HTLV type 1 (HTLV-1) and HTLV-2. In all coding regions, the similarity tends to be the lowest between STLV-PH969 and HTLV-1. However, in the long terminal repeat (LTR) region, the lowest similarity was found between STLV-PH969 and HTLV-2. The U3-R and R-U5 boundaries of the STLV-PH969 LTR were experimentally determined at nucleotides 268 and 524, respectively. This 695-bp LTR is 60 and 73 bp shorter than the LTRs of HTLV-1 and HTLV-2, respectively, but its general organization is similar to the one found in the HTLV-bovine leukemia virus genus. In the long region between the polyadenylation signal and the poly(A) site, sequence similarity with the HTLV-1 Rex-responsive element (RexRE) core and secondary structure prediction suggest the presence of a RexRE. The presence of three 21-bp repeats is conserved within the U3 region of HTLV-1, HTLV-2, and BLV. Only two direct repeats with similarity to these Tax-responsive elements were found in the STLV-PH969 LTR, which might suggest differences in the Tax-mediated transactivation of this virus. We conclude that STLV-PH969 has all the genes and genomic regions to suggest a replication cycle comparable to that of HTLV-1 and HTLV-2.
Inhalation injury to tracheal epithelium in an ovine model of cotton smoke exposure. Early phase (30 minutes).

The purpose of this study was to evaluate lung cell injury during the acute phase of smoke inhalation injury. A group of 10 sheep were anesthetized with halothane and pancuronium followed by endotracheal intubation. In the first experiment 5 sheep were given air (sham group) and 5 were insufflated with cooled cotton smoke with a modified bee smoker. In the second part of our study (Experiment 2) the animals were insufflated with the following number of smoke breaths: 1 x 12 (n = 3); 2 x 12 (n = 4); 3 x 12 (n = 4) 4 x 12 (n = 4); and sham control (n = 1). After 30 min the animals were killed with KCl and the trachea prepared for scanning, transmission electron, and light microscopy. Our initial observation with scanning electron microscopy revealed a large amount of mucus on the surface of the epithelia. Numerous ciliated cells had been sloughed from the epithelium and were observed on the surface of the remaining ciliated cells. The sloughed cells were intact, and the cilia remained on the apical cell surface. Light and transmission electron microscopy revealed that most goblet cells were in the process of extruding mucus. The cytoplasm of goblet and basal cells appeared normal. Ciliated cells had a slightly vesiculated cytoplasm, and many were in the process of being sloughed from the epithelial surface. In these cells desmosomal attachment had been separated. The light microscope evaluation of the tracheal epithelium showed there was no dose-dependent effect between the four treatment groups. (ABSTRACT TRUNCATED AT 250 WORDS)
Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation

Eleven mutant forms of staphylococcal nuclease with one or more defined amino acid substitutions have been analyzed by solvent denaturation by using intrinsic fluorescence to follow the denaturation reaction. On the basis of patterns observed in the value of m–the rate of change of log Kapp (the apparent equilibrium constant between the native and denatured states) with denaturant concentration—these proteins can be grouped into two classes. For class I mutants, the value of m with guanidine hydrochloride is less than the wild‐type value and is either constant or increases slightly with increasing denaturant; the value of m with urea is also less than wild type but shows a marked increase with increasing denaturant concentration, often approaching but never exceeding the wild‐type value. For class II mutants, m is constant and is greater than wild type in both denaturants, with the increase being consistently larger in guanidine hydrochloride than in urea. When double or triple mutants are constructed from members of the same mutant class, the change in m is usually the sum of the changes produced by each mutation in isolation. One plausible explanation for these altered patterns of denaturation is that chain‐chain or chain‐solvent interactions in the denatured state have been modified—interactions which appear to involve hydrophobic groups.
Biomechanical Evaluation of Transpedicular Nucleotomy With Intact Annulus Fibrosus

Study Design. Biomechanical testing of partially nucleotomized ovine cadaveric spines. Objective. To explore how the nucleus pulposus (NP) affects the biomechanical behavior of the intervertebral disc (IVD) by performing a partial nucleotomy via the transpedicular approach. Summary of Background Data. Mechanical loading represents a crucial part of IVD homeostasis. However, traditional regenerative strategies require violation of the annulus fibrosus (AF) resulting in significant alteration of joint mechanics. The transpedicular nucleotomy represents a suitable method to create a cavity into the NP, as a model to study IVD regeneration with intact AF. Methods. A total of 30 ovine-lumbar- functional spinal units (FSUs) (L1-L6) randomly assigned to 5 groups: control; transpedicular tunnel (TT); TT + polymethylmethacrylate (PMMA) to repair the bone tunnel; nucleotomy; nucleotomy + PMMA. Flexion/extension, lateral-bending, and axial-rotation were evaluated under adaptive displacement control. Axial compression was applied for 15 cycles of preconditioning followed by 1 hour of constant compression. Viscoelastic behavior was modeled and parameterized. Results. TT has minimal effects on rotational biomechanics. The nucleotomy increases ROM and neutral zone (NZ) displacement width whereas decreasing NZ stiffness. TT + PMMA has small effects in terms of ROM. Nucleotomy + PMMA brings ROM back to the control, increases NZ stiffness, and decreases NZ displacement width. The nucleotomy tends to increase the rate of early creep. TT reduces early and late damping. The use of PMMA increased late elastic stiffness (S2) and reduced viscous damping (&eegr;2) culminating in faster resolution of creep. Conclusion. Biomechanical properties of NP are crucial for IVD repair. This study demonstrated that TT does not affect rotational stability whereas partial nucleotomy with intact AF induce rotational instability, highlighting the central role of NP in early stages of IDD. Therefore, this model represents a successful platform to validate and optimize disc regeneration strategies. Level of Evidence: N/A
Isolation and molecular characterization of the ribosomal protein L6 homolog from Chlamydia trachomatis

The cloning of a Chlamydia trachomatis eukaryotic cell-binding protein reported earlier from our laboratory (R. Kaul, K. L. Roy, and W. M. Wenman, J. Bacteriol. 169:5152-5156, 1987) represents an artifact generated by nonspecific recombination of chromosomal DNA fragments. However, the amino terminus of this plasmid-encoded fusion product demonstrated significant homology to Escherichia coli ribosomal protein L6. By using a 458-bp PstI-HindIII fragment of recombinant pCT161/18 (representing the 5' end of the cloned gene), we isolated and characterized a C. trachomatis homolog of the ribosomal protein L6 gene of E. coli. Sequence analysis of an 1,194-bp EcoRI-SacI fragment that encodes chlamydial L6 (designated CtaL6e) revealed a 552-bp open reading frame comprising 183 amino acids and encodes a protein with a molecular weight of 19,839. Interestingly, complete gene homology between C. trachomatis serovars L2 and J, each of which exists as a single copy per genome, was observed. Expression of a plasmid-encoded gene product is dependent on the lac promoter, since no product was obtained if the open reading frame was oriented in opposition to the lac promoter. Immunoblotting of purified ribosomes revealed functional, as well as antigenic, homology between the E. coli and C. trachomatis ribosomal L6 proteins.
HEREDITARY ACHOLURIC JAUNDICEin a New Mutant Strain of Rats

A NEW mutant strain of rats was discovered in 1934 among the A. ~ breeding stock of the Connaught Laboratory animals. The mutant appears relatively yellow in color owing to an abnormal amount of bile pigment in its system; or in other words it is jaundiced. In animals other than man there appears to be no record of hereditary jaundice, save that of the rat, in which the icterus (yellow pigmentation) is evident at birth or shortly afterwards and persists throughout the life of the animals. The first indication of a new mutation relates to the observation of three young of a litter of thirteen which had a definite yellow tinge, while both parents were normal in appearance. The original rat stock is of Wistar origin, among which Dr. Helen Dean King has no record of such a mutation. "
The NL2KR System

In this paper we will describe the NL2KR system that translates natural language sentences to a targeted knowledge representation formalism. The system starts with an initial lexicon and learns meaning of new words from a given set of examples of sentences and their translations. We will describe the first release of our system with several examples.
Preparation of Potential Cell-Permeant Nucleoside-2′,3′-Cyclic Phosphate Precursors

Uridine-3′-phosphorothiolate triesters bearing lipophilic moieties were prepared via Michaelis-Arbuzov chemistry. Subsequent deprotection of the S-cholesteryl phosphorothiolate triester afforded the corresponding diester which underwent spontaneous Cyclization to cleanly afford uridine 2′,3′-cyclic phosphate. This transesterification reaction could be expedited by treatment with iodine under mild, neutral conditions.
A linearizing interface circuit with phase-error compensated direct-digital output for TMR-based angular position sensor

This paper proposes a simple and efficient electronic interface circuit for Tunneling Magneto-Resistance (TMR) based angular position sensor. The proposed circuit takes-in and processes the sine and cosine natured outputs of a TMR angle sensor using a novel methodology, and provides a linear output with angle for a full-circle range. The new methodology ensures that output has minimal dependence on phase-error of the oscillator employed in the circuit. The scheme also provides a digital output without using any separate analog-to-digital converters. Mathematical explanation of the proposed methodology and the interface circuit is presented. The basic working of the scheme is ascertained using simulation and emulation studies. The results show that the scheme has excellent output-linearity and very low dependence on the phase-error. Further, the circuit is tested with a prototype TMR angular position sensor unit. The overall system gave a low and nearly-constant non-linearity of around 0.55 % for different phase errors. Finally, comparison studies to show that the developed scheme offers better performance when compared with an existing high-performing scheme.