Miracle-dz/UniFAR-FTUs huggingface dataset:
Semi-quantitative polymerase chain reaction analysis of cytokine and cytokine receptor gene expression during thymic ontogeny.

Semi-quantitative, polymerase chain reaction (PCR) is used to uncover the patterns of cytokine transcription in the mouse thymus from day 14 to day 20 of gestation, a time period which includes many of the important events in thymic ontogeny. Interleukin 4 (IL-4), IL-7 and interferon gamma (IFN-gamma) mRNA is abundant from fetal day (Fd) 14-16, corresponding with the period of rapid proliferation of immature thymocytes in vivo. As the level of mRNA for these cytokines diminishes, the induction and increased expression of IL-3 and IL-2 occurs. The transcription of these cytokines correlates temporally with the period of proliferation-dependent phenotypic differentiation between Fd 16 and 20. The thymic epithelium (TE)-derived cytokines including IL-1alpha, IL-6 and granulocyte-macrophage colony-stimulating factor (GM-CSF) begin to be transcribed between Fd 14-15 and show peak mRNA abundance from Fd 16-20. IL-5, tumour necrosis factor alpha (TNF-alpha) and LT (lymphotoxin or TNF-beta) constitute a fourth group of cytokines, along with the IL-4 receptor (IL-4R), which are transcribed at an even level throughout the fetal period. The IL-2 receptor beta chain (IL-2Rbeta) and IL-10 show abundant mRNA from Fd 14-20 and have a peak level of mRNA content on Fd 16. Taken together, these studies uncover complex, overlapping patterns of cytokine gene expression. The mRNA abundance and pattern of expression of each cytokine or cytokine receptor may indicate the relative contribution that it makes to different stages of fetal thymic ontogeny.
Mateda-2.0: Estimation of Distribution Algorithms in MATLAB

This paper describes Mateda-2.0, a MATLAB package for estimation of distribution algorithms (EDAs). This package can be used to solve single and multi-objective discrete and continuous optimization problems using EDAs based on undirected and directed probabilistic graphical models. The implementation contains several methods commonly employed by EDAs. It is also conceived as an open package to allow users to incorporate different combinations of selection, learning, sampling, and local search procedures. Additionally, it includes methods to extract, process and visualize the structures learned by the probabilistic models. This way, it can unveil previously unknown information about the optimization problem domain. Mateda-2.0 also incorporates a module for creating and validating function models based on the probabilistic models learned by EDAs.
A Genetic Linkage Map of Cryptococcus neoformans variety neoformans Serotype D (Filobasidiella neoformans)

To construct a genetic linkage map of the heterothallic yeast, Cryptococcus neoformans (Filobasidiella neoformans), we crossed two mating-compatible strains and analyzed 94 progeny for the segregation of 301 polymorphic markers, consisting of 228 restriction site polymorphisms, 63 microsatellites, two indels, and eight mating-type (MAT)-associated markers. All but six markers showed no significant (P < 0.05) segregation distortion. At a minimum LOD score of 6.0 and a maximum recombination frequency of 0.30, 20 linkage groups were resolved, resulting in a map length of ∼1500 cM. Average marker density is 5.4 cM (range 1–28.7 cM). Hybridization of selected markers to blots of electrophoretic karyotypes unambiguously assigned all linkage groups to chromosomes and led us to conclude that the C. neoformans genome is ∼20.2 Mb, comprising 14 chromosomes ranging in size from 0.8 to 2.3 Mb, with a ratio of ∼13.2 kb/cM averaged across the genome. However, only 2 of 12 ungrouped markers hybridized to chromosome 10. The hybridizations revealed at least one possible reciprocal translocation involving chromosomes 8, 9, and 12. This map has been critical to genome sequence assembly and will be essential for future studies of quantitative trait inheritance.
An Investigation of the Consistency of Parental Occupational Information in UK Birth Records and a National Social Survey

In the UK new sources of administrative social science data are unfolding rapidly but the quality of these new forms of data for sociological research is yet to be established. We investigate the quality and consistency of the parental occupational information that is officially recorded on administrative birth records by undertaking a comparison with information collected from the same parents in the UK Millennium Cohort Study (MCS). We detect a large amount of missing information in the birth records and a range of inconsistencies. We present an empirical analysis of MCS data using parental social class measures derived both from the birth records and the survey to assess the effects of these discrepancies. We conclude that parental occupational information from administrative birth records should not be assumed, a priori, to be suitable for sociological analyses and that further research should be undertaken into their consistency and accuracy.
Emergence of a C-terminal seve 1 n amino acid elongation of NS1 around 1950 2 conferred a minor growth advantage to former seasonal influenza A viruses

Influenza A viruses circulating in humans from 1950 to 1987 featured a nonstructural (NS1) protein with a C-terminal extension of seven amino acids. The biological significance of this NS1 elongation remained elusive. We observed that replication kinetics of the wild-type virus A/Hong Kong/01/68 (H3N2) and a mutant encoding a truncated NS1 were indistinguishable in most experimental systems. However, wild-type virus outcompeted the mutant during mixed infections, suggesting that the NS1 extension conferred minor growth advantages. DOI: https://doi.org/10.1128/JVI.01271-13 Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-82276 Journal Article Accepted Version Originally published at: Lohrmann, F; Dijkman, R; Stertz, S; Thiel, V; Haller, O; Staeheli, P; Kochs, G (2013). Emergence of a C-terminal seve 1 n amino acid elongation of NS1 around 1950 2 conferred a minor growth advantage to former seasonal influenza A viruses. Journal of Virology, 87(20):11300-11303. DOI: https://doi.org/10.1128/JVI.01271-13
Autologous Cartilage Chip Transplantation Improves Repair Tissue Composition Compared With Marrow Stimulation

Background: Repair of chondral injuries by use of cartilage chips has recently demonstrated clinical feasibility. Purpose: To investigate in vivo cartilage repair outcome of autologous cartilage chips compared with marrow stimulation in full-thickness cartilage defects in a minipig model. Study Design: Controlled laboratory study. Methods: Six Göttingen minipigs received two 6-mm chondral defects in the medial and lateral trochlea of each knee. The two treatment groups were (1) autologous cartilage chips embedded in fibrin glue (ACC) (n = 12) and (2) marrow stimulation (MST) (n = 12). The animals were euthanized after 6 months, and the composition of repair tissue was quantitatively determined using histomorphometry. Semiquantitative evaluation was performed by means of the International Cartilage Repair Society (ICRS) II score. Collagen type II staining was used to further evaluate the repair tissue composition. Results: Significantly more hyaline cartilage was found in the ACC (17.1%) compared with MST (2.9%) group (P < .01). Furthermore, the ACC group had significantly less fibrous tissue (23.8%) compared with the MST group (41.1%) (P < .01). No significant difference in fibrocartilage content was found (54.7% for ACC vs 50.8% for MST). The ACC group had significantly higher ICRS II scores for tissue morphological characteristics, matrix staining, cell morphological characteristics, surface assessment, mid/deep assessment, and overall assessment (P < .05). The ACC-treated defects had significantly more collagen type II staining (54.5%) compared with the MST-treated defects (28.1%) (P < .05). Conclusion: ACC transplant resulted in improved quality of cartilage repair tissue compared with MST at 6 months postoperatively. Clinical Relevance: Further studies are needed to investigate ACC as a possible alternative first-line treatment for focal cartilage injuries in the knee.
Two‐dimensional gel electrophoresis in proteomics: Old, old fashioned, but it still climbs up the mountains

Proteomics has traditionnally used the separating power of two‐dimensional electrophoresis for the quantitative analysis of protein amounts in complex extracts. However, the limitations of this approach in terms of throughput and analyzable protein range have elicited the development of other proteomics approaches, based either on peptide separations instead of protein separations, or based on direct protein recognition and selection on dedicated arrays (protein chips). These recent methods seem very promising, and probably look more promising than they will ultimately be, just because their weaknesses are not fully characterized yet. The purpose of this paper is thus to highlight the strengths and weaknesses of all the proteomics approaches proposed to date and to try to deduce the respective niches in proteomics that these approaches will have in the future.
DNA Probe Method for the Detection of Specific Microorganisms in the Soil Bacterial Community

We developed a protocol which yields purified bacterial DNA from the soil bacterial community. The bacteria were first dispersed and separated from soil particles in the presence of polyvinylpolypyrrolidone, which removes humic acid contaminants by adsorption to this insoluble polymer. The soil bacteria were then collected by centrifugation and lysed by using a comprehensive protocol designed to maximize disruption of the various types of bacteria present. Total bacterial DNA was purified from the cell lysate and remaining soil contaminants by using equilibrium density gradients. The isolated DNA was essentially pure as determined by UV spectral analysis, was at least 48 kilobases long, and was not subject to degradation, which indicated that there was no contaminating nuclease activity. The isolated DNA was readily digested by exogenously added restriction endonucleases and successfully analyzed by slot blot and Southern blot hybridizations. Using single-stranded, 32P-labeled DNA probes, we could detect and quantitate the presence of a specific microbial population in the natural soil community on the basis of the presence of a DNA sequence unique to that organism. The sensitivity of our methodology was sufficient to detect Bradyrhizobium japonicum at densities as low as 4.3 × 104 cells per g (dry weight) of soil, which corresponds to about 0.2 pg of hybridizable DNA in a 1-μg DNA sample.
PySAL: the first 10 years

ABSTRACT This paper examines the field of regional science from the perspective of wider developments surrounding open-source software and the rising open-science movement. Regional science has been fairly isolated from these currents and a number of possible explanations for that isolation are identified. Opportunities that the emerging fields of data science and analytics afford for regional science are identified, and exemplar efforts leading the charge in engaging with these opportunities are highlighted.
Variations in Phase and Amplitude of Rhythmic Clock Gene Expression across Prefrontal Cortex, Hippocampus, Amygdala, and Hypothalamic Paraventricular and Suprachiasmatic Nuclei of Male and Female Rats

The molecular circadian clock is a self-regulating transcription/translation cycle of positive (Bmal1, Clock/Npas2) and negative (Per1,2,3, Cry1,2) regulatory components. While the molecular clock has been well characterized in the body’s master circadian pacemaker, the hypothalamic suprachiasmatic nucleus (SCN), only a few studies have examined both the positive and negative clock components in extra-SCN brain tissue. Furthermore, there has yet to be a direct comparison of male and female clock gene expression in the brain. This comparison is warranted, as there are sex differences in circadian functioning and disorders associated with disrupted clock gene expression. This study examined basal clock gene expression (Per1, Per2, Bmal1 mRNA) in the SCN, prefrontal cortex (PFC), rostral agranular insula, hypothalamic paraventricular nucleus (PVN), amygdala, and hippocampus of male and female rats at 4-h intervals throughout a 12:12 h light:dark cycle. There was a significant rhythm of Per1, Per2, and Bmal1 in the SCN, PFC, insula, PVN, subregions of the hippocampus, and amygdala with a 24-h period, suggesting the importance of an oscillating molecular clock in extra-SCN brain regions. There were 3 distinct clock gene expression profiles across the brain regions, indicative of diversity among brain clocks. Although, generally, the clock gene expression profiles were similar between male and female rats, there were some sex differences in the robustness of clock gene expression (e.g., females had fewer robust rhythms in the medial PFC, more robust rhythms in the hippocampus, and a greater mesor in the medial amygdala). Furthermore, females with a regular estrous cycle had attenuated aggregate rhythms in clock gene expression in the PFC compared with noncycling females. This suggests that gonadal hormones may modulate the expression of the molecular clock.
The Background Noise Environment During the 2013 Target and REverberation eXperiment

This paper presents an analysis of the time- and frequency-domain properties of a multiday series of background noise during the Target and REverberation eXperiment (TREX13) that took place off the coast of Panama City, FL, USA. Background noise was measured at two locations approximately 5 and 6 km south-east of the location of the <italic>R/V Sharp</italic> where monostatic reverberation was measured. The median spectral density level estimated for a frequency band centered at 2.7 kHz with a bandwidth of 1800 Hz was comparable to the median level at 3.5 kHz averaged over a bandwidth of 100 Hz; both were estimated to be 60 dB re 1 <inline-formula><tex-math notation="LaTeX">$\mu$</tex-math></inline-formula> Pa<inline-formula><tex-math notation="LaTeX">$^2$</tex-math></inline-formula>/Hz when averaged during the day or night. In contrast, the level at 4.5 kHz, estimated by averaging over a bandwidth of 100 Hz, increased by 14 dB at night. While the data suggest a degree of consistency in the background environment for the purposes of modeling, when assessing levels in the 80–8000 Hz frequency band, time of day was found to be influential. The median spectral levels presented may be used to assess the influence of background noise at a given time of day. Biological noise likely from fish was revealed to be a significant contributor to background noise at night, and daytime background noise levels were primarily influenced by wind.
Does "Fans Economy" Work for Chinese Pop Music Industry ?

China has become one of the largest entertainment markets in the world in recent years. Due to the success of Xiaomi, many Chinese pop music industry entrepreneurs believe "Fans Economy" works in the pop music industry. "Fans Economy" is based on the assumption that pop music consumer market could be segmented based on artists. Each music artist has its own exclusive loyal fans. In this paper, we provide an insightful study of the pop music artists and fans social network . Particularly, we segment the pop music consumer market and pop music artists respectively. Our results show that due to the Matthew Effect and limited diversity of consumer market, "Fans Economy" does not work for the Chinese pop music industry.
Identifying functions in binary code with reverse extended control flow graphs

In binary code analysis, current function identification approaches are challenged by functions without explicit call sites and handcrafted assembly without standard prologues/epilogues. We propose a new function representation called a reverse extended control flow graph (RECFG) and a RECFG‐based method for identifying functions in stripped binary code. A function has at least one return instruction (an instruction that makes the control flow leave a function). Therefore, return instructions are more reliable than the function prologues and epilogues used by traditional methods. We first build RECFGs from any values that can be interpreted as return instructions in a code range. Then, for each independent RECFG, the multiple‐decision method chooses a subgraph as the control flow graph of a function. A prototype tool is developed for evaluation on seven open source applications, 138 binaries in MASM32 code examples, and 292 binaries in Windows XP SP3. Experimental results show that the proposed method can identify functions that cannot be identified by current methods with high precision and stable recall. Copyright © 2015 John Wiley & Sons, Ltd.
Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure

Protein structure is dynamic: the intrinsic flexibility of polypeptides facilitates a range of conformational fluctuations, and individual protein chains can assemble into complexes. Proteins are also dynamic in evolution: significant variations in secondary, tertiary and quaternary structure can be observed among divergent members of a protein family. Recent work has highlighted intriguing similarities between these structural and evolutionary dynamics occurring at various levels. Here we review evidence showing how evolutionary changes in protein sequence and structure are often closely related to local protein flexibility and disorder, large‐scale motions and quaternary structure assembly. We suggest that these correspondences can be largely explained by neutral evolution, while deviations between structural and evolutionary dynamics can provide valuable functional insights. Finally, we address future prospects for the field and practical applications that arise from a deeper understanding of the intimate relationship between protein structure, dynamics, function and evolution.
Micro Assembly by Micro Resistance Welding with Electro-Thermal Actuators

Here micro resistance welding to assemble micro Ni structures with electro-thermal micro actuators is proposed and demonstrated. Since the contact point of two structures will have large contact resistance, high local temperature can be generated with current passing through due to Joule heating. In order to move the micro structure and provide welding pressure to generate proper contact resistance between two micro structures, bent-beam electro-thermal actuators are used here. By proper design on the size and the number of actuators, the feasible operation parameters on contact resistance and pressure are identified. It is shown that micro resistance welding can be achieved with the contact resistance from 4.6 Omega to 12 Omega at the contact pressure from 7.2 to 39.3 MPa.
Step-up unidirectional DC-DC autotransformer for HVDC applications

This paper studies a step-up unidirectional DC-DC autotransformer (UUDAT) topology that is dedicated for HVDC application. The UUDAT is composed by series connection of VSC and diode bridges. Because of employing DC-DC autotransformer technology, UUDAT is able to significantly reduce the power ratings of VSC, diode bridges and AC link compared with conventional unidirectional DC-AC-DC technology. Generic controller of UUDAT that enables successful DC power control is designed. DC fault response and DC fault isolation mechanism of UUDAT are analyzed. Cost penalty because of DC fault isolating capability are studied. Technical feasibly of UUDAT is verified by simulations on PSCAD/EMTDC. Results show that the UUDAT is promising to replace conventional step-up unidirectional DC-AC-DC technology under lower and medium DC voltage stepping ratio.
An Investigation of the English Collocational Knowledge of Jordanian Graduate Students

This study aims at investigating the English collocational knowledge of Jordanian graduate students and at analyzing quantitatively and qualitatively the collocational errors they made. The sample of the study involved thirty M.A TEFL graduate students at the Hashemite University in Jordan. The researcher adapted a completion test that measured students’ knowledge of four types of lexical collocations: free combination, restricted collocations, figurative idioms, and pure idioms. The results showed that free combination created the least amount of difficulty, whereas pure idioms were the most challenging. Additionally, students had unsatisfactory performance on restricted and figurative idioms. In general, the students’ deviant answers demonstrated their insufficient knowledge of the English collocations. It has been concluded that their errors can be attributed to first language interference.
Balance und posturale Kontrolle

Zusammenfassung Kaum eine Alltagshandlung ist möglich, wenn die Balance außer Kontrolle geraten ist. Dies jedoch geschieht bei einer Vielzahl neurologischer Erkrankungen häufig, insbesondere bei Schlaganfall. Stürze und Verletzungen drohen. Ihre Häufigkeit wird durch höheres Lebensalter noch verstärkt. Welche Therapiemaßnahmen können eingeleitet werden, um die posturale Kontrolle im Gang zu verbessern?
System design of the MeerKAT L - band 3D radar for monitoring near earth objects

This thesis investigates the current knowledge of small space debris (diameter less than 10 cm) and potentially hazardous asteroids (PHA) by the use of radar systems. It clearly identifies the challenges involved in detecting and tracking of small space debris and PHAs. The most significant challenges include: difficulty in tracking small space debris due to orbital instability and reduced radar cross-section (RCS), errors in some existing data sets, the lack of dedicated or contributing instruments in the Southern Hemisphere, and the large cost involved in building a high performance radar for this purpose. This thesis investigates the cooperative use of the KAT-7 (7 antennas) and MeerKAT (64 antennas) radio telescope receivers in a radar system to improve monitoring of small debris and PHAs was investigated using theory and simulations, as a cost effective solution. Parameters for a low cost and high performance radar were chosen, based on the receiver digital back-end. Data from such radars will be used to add to existing catalogues thereby creating a constantly updated database of near Earth objects and bridging the data gap that is currently being filled by mathematical models. Based on literature and system requirements, quasi-monostatic, bistatic, multistatic, single input multiple output (SIMO) radar configurations were proposed for radio telescope arrays in detecting, tracking and imaging small space debris in the low Earth orbit (LEO) and PHAs. The maximum dwell time possible for the radar geometry was found to be 30 seconds, with coherent integration limitations of 2 ms and 121 ms for accelerating and non-accelerating targets, respectively.