Miracle-dz/UniFAR-FTUs huggingface dataset:
Understanding the Role of Prdm12b in Zebrafish Development

IV LIST OF FIGURES . X LIST OF TABLES . XII LIST OF VIDEOS . XIII CHAPTER I: INTRODUCTION . 1 VERTEBRATE CENTRAL NERVOUS SYSTEM DEVELOPMENT . 2 The neural plate formation . 2 Transformation of neural plate into neural tube . 5 Neural tube patterning.6 PRDM FAMILY MEMBERS . 15 PRDMs as gene expression regulators . 16 Role of PRDMs in tissue specification and differentiation . 17 PRDMs in nervous system . 20 ZEBRAFISH LOCOMOTION CIRCUITRY . 24 Spinal cord neurons . 24 Motor behaviors in zebrafish . 27 CONTRIBUTION OF THIS WORK TO THE FIELD . 31 VII CHAPTER II: ZEBRAFISH PRDM12B ACTS INDEPENDENTLY OF NKX6.1 REPRESSION TO PROMOTE ENG1B EXPRESSION IN THE NEURAL TUBE P1 DOMAIN . 33 BACKGROUND . 34 METHODS . 37 Zebrafish care . 37 Generation of CRISPR/Cas9 mutant zebrafish lines . 37 Antisense morpholino oligonucleotide injections . 40 In situ RNA hybridization . 40 Luciferase reporter assays . 41 Co-immunoprecipitation and Western blotting . 42 Immunocytochemistry . 42 Behavioral analysis . 43 Genotyping . 43 RESULTS . 44 Germ line disruption of prdm12b blocks eng1b expression in the p1 domain . 44 The defective escape response in prdm12b mutants is caused by disruption of the Mauthner cell pathway . 58 Prdm12b acts as a repressor in vitro.66 Prdm12b interacts with the Bhlhe22 transcription factor and the EHMT2 methyltransferase.72 VIII bhlhe22 is not required for eng1b expression in the zebrafish p1 domain . 76 prdm12b does not maintain the p1 domain by repressing nkx6.1 . 81 DISCUSSION . 91 prdm12b germ line mutants recapitulate the phenotype observed using antisense-based approaches . 92 prdm12b is a bona fide transcriptional repressor . 93 An undefined domain persists at the p1 position in prdm12b mutants . 95 CONCLUSION.97 AUTHORS' CONTRIBUTIONS . 97 ACKNOWLEDGEMENTS . 98 CHAPTER III: DISCUSSION . 99 CORRELATION BETWEEN MORPHOLINO-INDUCED AND MUTANT PHENOTYPES IN PRDM12B LOCUS . 101 THE FATE OF THE REMAINING P1 DOMAIN IN PRDM12B MUTANTS IS UNDEFINED . 102 THE ROLE OF PRDM12B IN DORSOVENTRAL PATTERNING IS COMPLEX . 105 Further in vivo analysis of Prdm12b interaction partners namely Bhlhe22 and EHMT2/G9a is required . 105 What are the regulatory relationships of a subset of genes in the p0-p2? 109 IX THE RELATIONSHIP OF GENE EXPRESSION THROUGH THE P0-P2 DOMAIN MARKERS DOES NOT INVOLVE SIMPLE DIRECT INTERACTIONS . 112 REMAINING QUESTIONS AND FUTURE DIRECTIONS OF THIS WORK . 115 What are the prdm12b direct targets? 115 Do p1-derived neurons restrict Mauthner cells to fire only once? 117 CONCLUSION. 120 APPENDIX: THE EFFECT OF PRDM12B AND BHLHE22 MISEXPRESSION . 122 INTRODUCTION . 123 METHODS . 123 Zebrafish care . 123 Zebrafish were handled as discussed in Chapter II. 123 Zebrafish embryonic injections . 123 In situ RNA hybridization . 124 RESULTS . 125 Gain of function prdm12b and/or bhlhe22 does not affect eng1b expression . 125 DISCUSSION . 128 REFERENCES. 129
Effect of nerve growth factor and keratinocyte growth factor on wound healing of the sinus mucosa

The healing of the sinuses after sinus surgery is often compromised by the development of adhesions. The aim of this study was to determine whether nerve growth factor (NGF) and keratinocyte growth factor (KGF) aid epithelial and fibroblast wound healing after surgery. Two in vitro models were used to compare their effect on wound closure rates and expression of cell adhesion (E‐cadherin), tight junction formation (zona occludens‐1), cell proliferation (proliferative cell nuclear antigen and Ki67), and ciliogenesis (Foxj1 and β tubulin IVb) genes by real‐time reverse transcription polymerase chain reaction. Epithelial cells from sinonasal tissue were seeded in collagen‐coated Transwells, creating an air–liquid interface, and a submergent model was used for fibroblasts. In epithelial cells, NGF (20–50 ng/mL) significantly decreased wound areas to <40% compared with controls that were still 70% of their original sizes by 24 hours (p<0.05). E‐cadherin and zona occludens‐1 expression were up‐regulated by 20‐ and 2.5‐fold, respectively, relative to controls. KGF (5–100 ng/mL) slowed fibroblast proliferation by reducing (0.8‐fold) and Ki67 (0.25‐fold) expression. NGF (10 ng/mL) slowed Ki67 expression by 0.5‐fold. NGF accelerated in vitro epithelial wound closure while NGF and KGF reduced fibroblast proliferation.
Single Open-Slot Antenna for LTE/WWAN Smartphone Application

A single open-slot antenna for long term evolution (LTE)/ wireless wide area network (WWAN) operation is proposed for smartphone applications. To achieve dual-band operation, the narrow open-slot is fed by a simple 50-<inline-formula> <tex-math notation="LaTeX">$\Omega$ </tex-math></inline-formula> vertical feedline with two horizontally protruded feeding structures. To further attain good impedance matching for these two operating bands, an L-shaped metallic plate is used. From the measured results, good antenna efficiencies of more than 40% are demonstrated across the LTE/WWAN operation in the 698–960 MHz and 1710–2690 MHz bands.
[Using the SETQ system to evaluate and improve teaching qualities of clinical teachers].

OBJECTIVE To determine (a) the feasibility of implementing a system for the evaluation of teaching qualities (SETQ) of faculty in an academic medical centre, (b) the psychometric qualities of the questionnaires that are used for the generation of feedback and (c) how residents evaluate the teaching qualities of faculty members and how faculty rated themselves. DESIGN Questionnaire study. METHODS Residents evaluated the teaching qualities of faculty members and faculty also evaluated themselves. Specialty specific questionnaires were developed for both evaluations. The psychometric qualities of the questionnaires were determined by using exploratory factor analysis and by calculating the reliability coefficients of scale constructs and item-total correlation. Mean, median and range were calculated for all teaching aspects per training programme. RESULTS In the course of one year, 16 residency programmes in our academic medical centre implemented the SETQ system for the evaluation of teaching faculty. 398 faculty members and 314 residents were invited to (self-) evaluate; the response rates were 80.9% and 73.6% respectively. Residents conducted 2,520 evaluations in total. Factor analysis resulted in the definition of 5 teaching domains: 'learning climate', 'professional attitude towards residents', 'communication of learning goals', 'evaluation of residents' and 'feedback to residents'. Item-total correlation and reliability were high for both the residents' questionnaire and the self-evaluation questionnaire (Cronbach's alpha: > 0.70), except for the educational aspect 'learning climate' on the self-evaluation questionnaire (alpha: 0.67) Faculty members were rated positively, but the self-evaluation of faculty members was slightly less positive. For both groups 'professional attitude towards residents' was the highest scoring teaching domain and 'communication of learning goals' the lowest one. CONCLUSION Implementing a system for the evaluation of teaching qualities (SETQ) of faculty in an academic hospital was proven feasible. The psychometric qualities of the underlying instruments was sufficient to good. Teaching faculty were evaluated positively, although interdepartmental variations existed.
Review of anti-demagnetization design method for vehicle permanent magnet motor

Based on the irreversible demagnetization of the permanent magnet (PM) in vehicle permanent magnet motor (PMM), the demagnetization mechanism of PM is presented and the main factor of vehicle high density PMM demagnetization is analyzed in this paper. The design, analysis and optimization method of anti-demagnetization of PMM at home and abroad are proposed. The advantages and disadvantages of anti-demagnetization analysis method are investigated. At the same time, the solutions and research directions are pointed out, and these works will provide useful information for anti-demagnetization design and contribute to the development of the anti-demagnetization technology for vehicle PMM.
Overlapping Signals for Transcription and Replication at the 3′ Terminus of the Vesicular Stomatitis Virus Genome

ABSTRACT Transcription and replication signals within the negative-sense genomic RNA of vesicular stomatitis virus (VSV) are located at the 3′ terminus. To identify these signals, we have used a transcription- and replication-competent minigenome of VSV to generate a series of deletions spanning the first 47 nucleotides at the 3′ terminus of the VSV genome corresponding to the leader gene. Analysis of these mutants for their ability to replicate showed that deletion of sequences within the first 24 nucleotides abrogated or greatly reduced the level of replication. Deletion of downstream sequences from nucleotides 25 to 47 reduced the level of replication only to 55 to 70% of that of the parental template. When transcription activity of these templates was measured, the first 24 nucleotides were also found to be required for transcription, since deletion of these sequences blocked or significantly reduced transcription. Downstream sequences from nucleotides 25 to 47 were necessary for optimal levels of transcription. Furthermore, replacement of sequences within the 25 to 47 nucleotides with random heterologous nonviral sequences generated mutant templates that replicated well (65 to 70% of the wild-type levels) but were transcribed poorly (10 to 15% of the wild-type levels). These results suggest that the minimal promoter for transcription and replication could be as small as the first 19 nucleotides and is contained within the 3′-terminal 24 nucleotides of the VSV genome. The sequences from nucleotides 25 to 47 may play a more important role in optimal transcription than in replication. Our results also show that deletion of sequences within the leader gene does not influence the site of transcription reinitiation of the downstream gene.
Surgical Robot for Single-Incision Laparoscopic Surgery

This paper introduces a novel surgical robot for single-incision laparoscopic surgeries. The robot system includes the cone-type remote center-of-motion (RCM) mechanism and two articulated instruments having a flexible linkage-driven elbow. The RCM mechanism, which has two revolute joints and one prismatic joint, is designed to maintain a stationary point at the apex of the cone shape. By placing the stationary point on the incision area, the mechanism allows a surgical instrument to explore the abdominal area through a small incision point. The instruments have six articulated joints, including an elbow pitch joint, which make the triangulation position for the surgery possible inside of the abdominal area. The presented elbow pitch structure is similar to the slider-crank mechanism but the connecting rod is composed of a flexible leaf spring for high payload and small looseness error. We verified the payload of the robot is more than 10 N and described preliminary experiments on peg transfer and suture motion by using the proposed surgical robot.
Association of trans fatty acid intake with metabolic risk factors among free-living young Japanese women.

OBJECTIVE We examined cross-sectional associations of total, hydrogenated, and natural trans fatty acid intake with selected metabolic risk factors in young Japanese women. METHODS Subjects were 1136 Japanese female dietetic students aged 18-22 years. Dietary intake was estimated using a validated, self-administered diet history questionnaire. Associations between trans fatty acid intake and metabolic risk factors were examined with multivariate linear regression analysis, with control for potential covariates. Dietary covariates included intake of energy, total fat, and saturated fatty acids (model 1); monounsaturated fatty acids instead of saturated fatty acids (model 2); and polyunsaturated fatty acids instead of saturated fatty acids (model 3). RESULTS Mean (standard deviation) total trans fatty acid intake was 0.90% (0.30%) of total energy. Hydrogenated trans fatty acids contributed 77% of total trans fatty acid intake. Total trans fatty acid intake was significantly and positively associated with waist circumference, triacylglycerol, and glycated hemoglobin, except in the analysis of triacylglycerol with adjustment for monounsaturated fatty acids. No associations were found between total trans fatty acid intake and body mass index, cholesterol, or glucose. Hydrogenated trans fatty acid intake was significantly and positively associated only with waist circumference and glycated hemoglobin. No association was observed for natural trans fatty acid intake. CONCLUSION hydrogenated trans fatty acid intake was positively associated with several metabolic risk factors among free-living young Japanese women with relatively low intake.
A Distant Multipath Routing Method for Reliable Wireless Multi-Hop Data Transmission

In a wireless multi-hop network between a source node (S) and a destination node (D), multipath routing in which S redundantly sends the same packets to D through multiple routes at the same time is effective for enhancing the reliability of the wireless data transmission by means of route diversity. However, when applying the multipath routing to a factory where huge robots are moving around, if closer multiple routes are selected, the probability that they are blocked by the robots at the same time becomes higher, so the reliability in terms of packet loss rate cannot be enhanced. This paper proposes a multipath routing method which can select physically distant multiple routes without any knowledge on the locations of nodes. Maximizing the metric composed of "the distance between routes" and "the route quality" by means of scalarization in multi-objective maximization problem, the proposed method can adaptively control the topologies of selected routes between S and D.
Emergence and Dissemination of Quinolone-ResistantEscherichia coli in the Community

ABSTRACT We studied the evolution of resistance to quinolones inEscherichia coli from 1992 to 1997 in Barcelona, Spain. An increasing proportion of quinolone-resistant E. coli (QREC) infections was observed. QREC strains were more common in patients with nosocomial infections but also increased in patients with community-acquired infections (9% in 1992 to 17% in 1996). Seventy (12%) of 572 episodes of E. coli bacteremia were due to QREC. Factors significantly associated with QREC bacteremia were the presence of underlying disease, recent exposure to antibiotics, and bacteremia of unknown origin. In the multivariate analysis, only prior exposure to antimicrobial agents (P < 0.001; odds ratio [OR] = 2), specifically, to quinolones (P < 0.001; OR = 14), and the presence of a urinary catheter (P < 0.001; OR = 2) were significantly associated with QREC bacteremia. Among 16 QREC isolates from cultures of blood of community origin selected at random, 13 different pulsed-field gel electrophoresis patterns were recognized, showing the genetic diversity of these isolates and in turn indicating the independent emergence of QREC in the community. The prevalence of QREC in the feces of healthy people was unexpectedly high (24% in adults and 26% in children). A survey of the prevalence of QREC of avian and porcine origin revealed a very high proportion of QREC in animal feces (up to 90% of chickens harbored QREC). The high prevalence of QREC in the stools of healthy humans in our area could be linked to the high prevalence of resistant isolates in poultry and pork.
Chicken eggshell as suitable calcium source at home

Abstract Aim: Taken into consideration that the deficiency of calcium (Ca) in the diet is a common problem, the aim of this work was to study the chicken eggshell as Ca source at home. It was evaluated: (1) different mechanisms to process eggshells and find an easy way to determine the required amount of Ca at home and; (2) the flavor and the texture for eggshell fortified food. Methods: Chemical and mechanical methods of eggshell processing were evaluated. Changes in flavor and texture were evaluated in volunteers coordinated by a professional chef. Results: A single eggshell contains 2.07 ± 0.18 g of Ca; therefore half an eggshell could provide the amount of Ca needed by adult human beings per day. The best way to use chicken eggshell as Ca dietary supplement is powdered to add to bread, pizza or spaghetti as there were small changes in texture and no changes in flavor.
Shear Stress–Dependent Regulation of the Human &bgr;-Tubulin Folding Cofactor D Gene

Abstract— The flowing blood generates shear stress at the endothelial cell surface. The endothelial cells modify their phenotype by alterations in gene expression in response to different levels of fluid shear stress. To identify genes involved in this process, human umbilical vein endothelial cells were exposed to laminar shear stress (venous or arterial levels) in a cone-and-plate apparatus for 24 hours. Using the method of RNA arbitrarily primed polymerase chain reaction, we cloned a polymerase chain reaction fragment representing an mRNA species downregulated by arterial compared with venous shear stress (shear stress downregulated gene-1, SSD-1). According to Northern blot analysis, corresponding SSD-1 cDNA clones revealed a similar, time-dependent downregulation after 24 hours of arterial shear stress compared with venous shear stress or static controls. Three SSD-1 mRNA species of 2.8, 4.1, and 4.6 kb were expressed in a tissue-specific manner. The encoded amino acid sequence of the human endothelial SSD-1 isoform (4.1-kb mRNA species) revealed 80.4% identity and 90.9% homology to the bovine &bgr;-tubulin folding cofactor D (tfcD) gene. Downregulation of tfcD mRNA expression by shear stress was defined at the level of transcription by nuclear run-on assays. The tfcD protein was downregulated by arterial shear stress. The shear stress–dependent downregulation of tfcD mRNA and protein was attenuated by the NO synthase inhibitor N&ohgr;-nitro-l-arginine methyl ester. Furthermore, the NO donor DETA-NO downregulated tfcD mRNA. Because tfcD was shown to be a microtubule-destabilizing protein, our data suggest a shear stress–dependent regulation of the microtubular dynamics in human endothelial cells.
Low-Cost Multimode Patch Antenna for Dual MIMO and Enhanced Localization Use

This communication proposes a simple, low-cost multimode patch antenna combining good multi-in multi-out (MIMO) performance with precise angle of arrival (AoA) estimation. The AoA is based on the monopulse antenna concept; however, unlike in radar applications, the necessity for complex circuitry is replaced by the intrinsic properties of even and odd resonant patch modes. This capability is advantageous for future “Internet of Things” antennas, embedded into low-cost and size-constrained devices. The envelope correlation coefficient, measured in an anechoic chamber, is below 1.5%, ensuring good MIMO performance. An exemplary addition to localization algorithm exploiting antenna properties is demonstrated.
How to Evaluate the Effectiveness of Catheter-Directed Thrombolytic Therapy in Pulmonary Embolism

We congratulate the authors on their successful study. Although a relatively new method, the catheter-directed ultrasound-accelerated thrombolysis (USAT) was reported in various studies to yield satisfactory results in the treatment of acute pulmonary embolism. As in the present study, the effectiveness of the treatment has been evaluated on the basis of the degree of thrombolysis confirmed by computed tomography (CT) in the clot impacted in the pulmonary artery following the therapy. However, Engelhardt et al assessed the right–left ventricular (RV/LV) diameter ratios on CT, detecting a decrease in the former ratio depending on the right ventricular shrinkage due to regression of the right ventricular failure following USAT therapy. Of the patients in whom we performed USAT in our clinic, we noted a dramatic improvement in the symptoms and a decrease in the RV/LV ratio following the procedure in one, although a noncomplete lysis was confirmed on postoperative CT in the pulmonary arterial clot. It was reported upon performing this procedure that a complete disappearance of the pulmonary arterial thrombus was revealed by control CT and that resolution of the patients’ symptoms was achieved following the treatment. We believe that disclosing the presence or absence of any probable difference between preoperative and postoperative RV/LV ratios in this study would be much more illuminating with respect to the results of the treatment.
Bottom-up/Top-down Geometric Object Reconstruction with CNN Classification for Mobile Education

Geometric objects in educational materials are often illustrated as 2D line drawings, which results in the loss of depth information. To alleviate the problem of fully understanding the 3D structure of geometric objects, we propose a novel method to reconstruct the 3D shape of a geometric object illustrated in a line drawing image. In contrast to most existing methods, ours directly take a single line drawing image as input and generate a valid sketch for reconstruction. Given a single input line drawing image, we ﬁrst classify the geometric object in the image with convolution neural network (CNN). More speciﬁcally, we pre-train the model with simulated images to alleviate the problems of data collection and unbalanced distribution among different classes. Then, we generate the sketch of the geometric object with our proposed bottom-up and top-down scheme. Finally, we ﬁnish reconstruction by minimizing an objective function of reconstruction error. Extensive experimental results demonstrate that our method performs signiﬁcantly better in both accuracy and efﬁciency compared with the existing methods.
A signature-based algorithm for computing Gröbner bases in solvable polynomial algebras

Signature-based algorithms, including F5, F5C, G2V and GVW, are efficient algorithms for computing Gröbner bases in commutative polynomial rings. In this paper, we present a signature-based algorithm to compute Gröbner bases in solvable polynomial algebras which include usual commutative polynomial rings and some non-commutative polynomial rings like Weyl algebra. The generalized Rewritten Criterion (discussed in Sun and Wang, ISSAC 2011) is used to reject redundant computations. When this new algorithm uses the partial order implied by GVW, its termination is proved without special assumptions on computing orders of critical pairs. Data structures similar to F5 can be used to speed up this new algorithm, and Gröbner bases of syzygy modules of input polynomials can be obtained from the outputs easily. Experimental data show that most redundant computations can be avoided in this new algorithm.