Miracle-dz/UniFAR-FTUs huggingface dataset:
Automation of single-cell techniques in neural tissue

The highly heterogeneous nature of cells in the context of native tissue environments necessitates the development of tools and techniques that can manipulate and analyze samples with single-cell resolution. While the past decades have seen significant progress in analyzing individual cells in tissue, both electrically and morphologically, the ability to genetically manipulate and biochemically analyze such cells in a high-throughput manner has seen only limited advances, and therefore a significant technological gap in accessing cells with single-cell specificity in tissue remains. We present a system design and workflow that fills in this gal) in technology through the implementation of precision automation and redesign of standard biological techniques, resulting in greatly improved throughput while maintaining single-cell accuracy and precision. This thesis comprises three parts: First we discuss the design and implementation of an expandable comlputer-cont rolled automation system enabling the rapid maneuvering and targeting of inicropipettes within tissue environments as well as a methodology for cleaning and reuse of these lnicropipettes to enable significant gains in throughput. Second we apply this automation to transfecting neurons in brain slices with DNA and RNA for subsequent analysis with greater throughput than previous methods. Third, we apply our automation to collecting the contents of single neurons embedded in relevant tissue environments for molecular analysis. The work presented greatly improves the throughput of traditional single-cell methods of transfection and cell-sampling by between one and two orders of magnitude and fills in a gap in the workflow of the rapidly expanding field of single-cell analysis. Thesis Supervisor: Mehmet Fatih Yanik Title: Assistant Professor of Electrical Engineering
The ascidian pigmented sensory organs: structures and developmental programs

The recent advances on ascidian pigment sensory organ development and function represent a fascinating platform to get insight on the basic programs of chordate eye formation. This review aims to summarize current knowledge, at the structural and molecular levels, on the two main building blocks of ascidian light sensory organ, i.e. pigment cells and photoreceptor cells. The unique features of these structures (e.g., simplicity and well characterized cell lineage) are indeed making it possible to dissect the developmental programs at single cell resolution and will soon provide a panel of molecular tools to be exploited for a deep developmental and comparative‐evolutionary analysis. genesis 53:15–33, 2015. © 2014 Wiley Periodicals, Inc.
The retrieval of learned sequences engages the hippocampus: Evidence from fMRI

Computational models suggest that the hippocampus plays an important role in the retrieval of sequences. However, empirical evidence supporting hippocampal involvement during sequence retrieval is lacking. The current study used functional magnetic resonance imaging (fMRI) to examine the role of the human hippocampus during the learning and retrieval of sequences. Participants were asked to learn four sequences comprised of six faces each. An overlapping condition, where sequences shared common elements, was comprised of two sequences in which two identical faces were shown as the middle images of both sequences. A nonoverlapping condition contained two sequences that did not share any faces between them. A third random condition contained two sets of six faces that were always presented in a random order. The fMRI data were split into a learning phase and an experienced phase based upon each individual's behavioral performance. Patterns of hippocampal activity during presentation, delay, and choice periods were assessed both during learning (learning phase) and after subjects learned the sequences to criteria (experienced phase). The results revealed hippocampal activation during sequence learning, consistent with previous findings in rats and humans. Critically, the current results revealed hippocampal activation during the retrieval of learned sequences. No difference in hippocampal activation was seen between the overlapping and nonoverlapping sequences during either sequence learning or retrieval of sequences. The results extend our current knowledge by providing evidence that the hippocampus is active during the retrieval of learned sequences, consistent with current computational models of sequence learning and retrieval. © 2009 Wiley‐Liss, Inc.
Phosphoproteomics: A possible route to novel biomarkers of breast cancer

Proteomics is rapidly transforming the way that cancer and other pathologies are investigated. The ability to identify hundreds of proteins and to compare their abundance in different clinical samples presents a unique opportunity for direct identification of novel disease markers. Furthermore, recent advances allow us to analyse and compare PTMs. This gives an additional dimension for defining a new class of protein biomarker based not only on abundance and expression but also on the occurrence of covalent modifications specific to a disease state or therapy response. Such modifications are often a consequence of the activation/inactivation of a particular disease related pathway. In this review we evaluate the available information on breast cancer related protein‐phosphorylation events, illustrating the rationale for investigating this PTM as a target for breast cancer research with eventual clinical relevance. We present a critical survey of the published experimental strategies to study protein phosphorylation on a system wide scale and highlight recent specific advances in breast cancer phosphoproteomics. Finally we discuss the feasibility of establishing novel biomarkers for breast cancer based on the detection of patterns of specific protein phosphorylation events.
The mediating impact of coping style on stress perception for parents of individuals with intellectual disabilities

Research reveals that parents of individuals with intellectual disabilities experience more stress than parents of persons of normal development. The majority of previous research has measured direct relationships between stress variables and stress perception and little attention has been given to the impact of mediating variables. The present study utilized an indirect pathway model to examine the mediating influence of coping style on the relationship between social support, severity of child disability, parental optimism and stress perception for these parents. Parents of individuals receiving mental health services through an agency in Southeastern Michigan participated in the study. Results indicated that coping style partially mediated the relationship between social support and stress perception for parents of individuals with intellectual disabilities.
Auxin 2016: a burst of auxin in the warm south of China

The luxurious vegetation at Sanya, the most southern location in China on the island of Hainan, provided a perfect environment for the ‘Auxin 2016’ meeting in October. As we review here, participants from all around the world discussed the latest advances in auxin transport, metabolism and signaling pathways, highlighting how auxin acts during plant development and in response to the environment in combination with other hormones. The meeting also provided a rich perspective on the evolution of the role of auxin, from algae to higher plants. Summary: This Meeting Review discusses the research that was presented at the ‘Auxin 2016’ meeting, highlighting the latest advances in understanding auxin transport, metabolism and signaling.
The dual and opposite role of the TM6SF2‐rs58542926 variant in protecting against cardiovascular disease and conferring risk for nonalcoholic fatty liver: A meta‐analysis

The aim of this work was to estimate the strength of the effect of the TM6SF2 E167K (rs58542926 C/T) variant on blood lipid traits and nonalcoholic fatty liver disease (NAFLD) across different populations. We performed a systematic review by a meta‐analysis; literature searches identified 10 studies. The rs58542926 exerts a significant role in modulating lipid traits, including total cholesterol (TC), low‐density lipoprotein cholesterol (LDL‐C), triglycerides (TG), and NAFLD. However, this influence on lipids and NAFLD is opposite between genotypes in the dominant model of inheritance. Pooled estimates of random effects in 101,326 individuals showed that carriers of the minor T allele (EK+KK individuals), compared with subjects homozygous for the ancestral C allele (EE genotype), are protected from cardiovascular disease (CVD), showing lower levels of TC, LDL‐C, and TG; the differences in mean ± standard error (mg/dL) are −8.38 ± 1.56, −3.7 ± 0.9, and −9.4 ± 2.1, respectively. The rs58542926 variant was not associated with high‐density lipoprotein cholesterol in a large sample (n = 91,937). In contrast, carriers of the T allele showed a moderate effect on the risk of NAFLD (odds ratio: 2.13; 95% confidence interval: 1.36–3.30; P = 0.0009; n = 3273) and approximately ∼2.2% higher lipid fat content when compared with homozygous EE (n = 3,413). Conclusions: The rs58542926 appears to be an important modifier of blood lipid traits in different populations. As a challenge for personalized medicine, the C‐allele, which has an overall frequency as high as 93%, is associated with higher blood lipids, whereas the T allele confers risk for NAFLD; in turn, CVD and NAFLD are strongly related outcomes. Although the variant confers protection against CVD at the expense of an increased risk of NAFLD, it does not explain the link between these two complex diseases. (Hepatology 2015;62:1742–1756)
KIM – a semantic platform for information extraction and retrieval

The KIM platform provides a novel Knowledge and Information Management framework and services for automatic semantic annotation, indexing, and retrieval of documents. It provides a mature and semantically enabled infrastructure for scalable and customizable information extraction (IE) as well as annotation and document management, based on GATE.General Architecture for Text Engineering (GATE) (http://gate.ac.uk), leading NLP and IE platform developed at the University of Sheffield. Our understanding is that a system for semantic annotation should be based upon a simple model of real-world entity concepts, complemented with quasi-exhaustive instance knowledge. To ensure efficiency, easy sharing, and reusability of the metadata we introduce an upper-level ontology. Based on the ontology, a large-scale instance base of entity descriptions is maintained. The knowledge resources involved are handled by use of state-of-the-art Semantic Web technology and standards, including RDF(S) repositories, ontology middleware and reasoning. From a technical point of view, the platform allows KIM-based applications to use it for automatic semantic annotation, for content retrieval based on semantic queries, and for semantic repository access. As a framework, KIM also allows various IE modules, semantic repositories and information retrieval engines to be plugged into it. This paper presents the KIM platform, with an emphasis on its architecture, interfaces, front-ends, and other technical issues.
Mix Design of Self Compacting Concrete Based on Ultra High Compressive Strength Flow Mortar Mix

Mix design of Self Compacting Concrete or SCC is not straight forward because many parameters control its rheological properties. The case becomes more complicated if high compressive strength is also to be achieved. Therefore simpler approach is used, that is by firstly determining the flow mortar mix which is easier to be designed even with the requirement of ultra-high compressive strength. The mix design of SCC is then determined by simply adding the coarse aggregate with a certain amount of that mortar mix. In this research the ultra-high compressive strength flow mortar was made of Type I cement, 15% of cement weight silica fume, weight ratio of cement and curve No IV sand was 1: 0.35. The water-cementious ratio was 0.22 and the amount of plasticizer was 1.3%, 1.4%, 1.5% and 1.6% of the cement weight. For the SCC, the used coefficient was taken to be 1.4, 1.6, and 1.8 of the volume of that aggregate void for mortars, the aggregate value was at the volume of the remaining count of mortar and its size was 4.8 mm - 9.6 mm. Test results show that the mortar flow ability was 170 mm, 180 mm, 220 mm and 250 mm, where the achieved compressive strength was 83.1 MPa, 96.8 MPa, 111.4 MPa, and 135.5 MPa respectively. Mortar mix with 1.6% super plasticizer was then used for making the SCC and the results show that the concrete flow were 460 mm, 580 mm and 660 mm and the compressive strength were 88.2 MPa, 100.0 MPa, and 97.9 MPa. It can be concluded that using this simpler approach the SCC can have 580 mm flow and 100 MPa compressive strength
ERF and ETV3L are retinoic acid-inducible repressors required for primary neurogenesis

Cells in the developing neural tissue demonstrate an exquisite balance between proliferation and differentiation. Retinoic acid (RA) is required for neuronal differentiation by promoting expression of proneural and neurogenic genes. We show that RA acts early in the neurogenic pathway by inhibiting expression of neural progenitor markers Geminin and Foxd4l1, thereby promoting differentiation. Our screen for RA target genes in early Xenopus development identified Ets2 Repressor Factor (Erf) and the closely related ETS repressors Etv3 and Etv3-like (Etv3l). Erf and Etv3l are RA responsive and inhibit the action of ETS genes downstream of FGF signaling, placing them at the intersection of RA and growth factor signaling. We hypothesized that RA regulates primary neurogenesis by inducing Erf and Etv3l to antagonize proliferative signals. Loss-of-function analysis showed that Erf and Etv3l are required to inhibit proliferation of neural progenitors to allow differentiation, whereas overexpression of Erf led to an increase in the number of primary neurons. Therefore, these RA-induced ETS repressors are key components of the proliferation-differentiation switch during primary neurogenesis in vivo.
Contribution of a Cyclonic-Based Liquid Air Collector for Detecting Aspergillus Fumigatus by QPCR in Air Samples

Fungal infections represent a constant threat in hospitals, especially for high-risk patients hospitalized in hematology and bone marrow transplant units. While routine air sampling to predict the fungal contamination risk is discussed by some authors,(1,2) French hospital guidelines specify that each hospital is responsible for the air it provides to patients and that air control efficiency must be monitored by specific methodologies. (3) Traditional monitoring involves impacted culture media that are incubated for several days so that the fungal species may grow and be identified on the basis of macroscopic and microscopic criteria. (4) A variety of portable air impactors are commercially available and validated,(5,6) but these systems are limited by their link with culture techniques, involving a time-lapse to results of around 7 days and by a maximal sampling rate of 100 L/min. As optimal environmental monitoring requires large sample sizes and fast, accurate detection of microorganisms contained within the samples,(7,8) new techniques concurring with these characteristics are regularly evaluated. Quantitative polymerase chain reaction (QPCR) represents a very attractive alternative to culture techniques as it allows Aspergillus fumigatus, which is the preponderant etiologic agent of invasive aspergillosis, to be specifically detected in under 2 days. Reducing the time to results is key to permit intervention to prevent Aspergillus exposure in immunocompromised patients. In this way, QPCR was previously used to amplify Aspergillus fumigatus DNA on various substrates, such as tap water,(9) carpets,(7) air filters,(10) and impacted lowmelt agar plates. (11) A new device, the Coriolis μ air sampler (Bertin Technologies, Montigny, France), based on a cyclonic system, was recently proposed for collecting large volumes of air on liquid medium quickly. This device was previously assessed for different areas other than fungal aero-contamination monitoring: analysis of pollen grain distribution(12,13) and detection of Pneumocystis jiroveci DNA by QPCR. (14) A preliminary study was carried out to test this cyclonic-based liquid device, combined with QPCR, and to assess its performance for detecting A. fumigatus DNA.
Plasma for Laboratory Diagnostics

Main clinical and scientific aspects of methodology how to choose the right sample for testing to be involved in Plasma for Laboratory Diagnostics chapter as plasma is in use sufficiently widely. Different approach by clinical and research laboratories formed the necessity to discuss the basic laboratory terms and conditions to obtain correct results. Evaluation of preanalytical variables with impact on handling, processing and storage of samples with subsequent meaning for laboratory test results should be known by physicians, biomedical scientists, laboratory technicians and so on. The impact of chemical additives for diagnostics tools, the differences between plasma and serum samples for different laboratory tests and the subsequent analysis, manage - ment and traceability of specimens with standardisation value should be taken into account.
Controllable wettability of metallic surfaces via micro-nano structure fabricated by femtosecond laser

Micro-pits array structure, micro-gratings structure covered with finer nanostructures were generated on titanium surfaces using femtosecond laser pulse. The wetting behavior of the two types of surface structures were studied. Micropits array structure with a size of dozens of microns exhibits hydrophilic properties, and the hydrophilicity increased with increasing the number of laser pulses. Micro-gratings structure covered with finer nanostructures exhibits hydrophobic properties, and the hydrophobicity increased with decreasing the laser energy density. The results demonstrated that wettability of metallic surface can be facilely controlled by adjusting the femtosecond laser processing parameters. The formation processes of the two types of surface microstructures as well as the underlying mechanisms for their special wettability are also discussed. This research might provide a facile controllable strategy to realize special wettability for metal or other solid surfaces, even expand the functions and applications of metals.
Association between Vgamma2Vdelta2 T cells and disease progression after infection with closely related strains of HIV in China.

BACKGROUND Human immunodeficiency virus (HIV) infection and disease are accompanied by decreases in the absolute number and function of Vgamma2Vdelta2 T cells, suggesting that this subset of cells may play an important role in controlling disease. We performed a cross-sectional study involving HIV-infected former blood donors and assessed the association between Vgamma2Vdelta2 T cells and markers of disease progression. METHODS Changes in Vgamma2Vdelta2 T cell count and function were compared between HIV-infected individuals and healthy blood donors using the Mann-Whitney U test. The relationships between Vgamma2Vdelta2 T cell count, plasma viral load, and CD4 T cell count were analyzed using the Spearman correlation. RESULTS We found significant positive correlations between CD4 T cell count and both total Vgamma2Vdelta2 T cell count (P<.001) and functional (isopentenyl pyrophosphate-responsive) Vgamma2Vdelta2 T cell count (P<.001). We found significant reverse correlations between viral load and both total Vgamma2Vdelta2 T cell count (P<.05) and functional Vgamma2Vdelta2 T cell count (P<.05). CONCLUSIONS The association of Vgamma2Vdelta2 T cells with disease progression in 146 HIV-infected participants supports the view that intact Vgamma2Vdelta2 T cell populations are important for controlling HIV disease.
From Faux-Social to Pro-Social: The Mediating Role of Copresence in Developing Expectations of Social Support in a Game

Social network games—games that incorporate network data from social network sites—heavily rely on helping behavior between players as a central mechanism of play. Does this “faux social” behavior still generate expectations of social support among players? An experiment (N = 88) was conducted to examine the effect of helping on copresence and perceived social support between strangers playing the Facebook game Cityville. Three types of social support were examined: instrumental support within the game, instrumental support outside of the game, and emotional support. Findings indicate that the simple action of being helped in a game generates copresence, the feeling of proximity in a virtual environment. Copresence was a positive predictor of all three types of perceived social support but had highest explanatory power for instrumental support within the game.
Incremental Organization for Data Recording and Warehousing

Data warehouses and recording systems typically have a large continuous stream of incoming data, that must be stored in a manner suitable for future access. Access to stored records is usually based on a key. Organizing the data on disk as the data arrives using standard techniques would result in either (a) one or more I/OS to store each incoming record (to keep the data clustered by the key), which is too expensive when data arrival rates are very high, or (b) many I/OS to locate records for a particular customer (if data is stored clustered by arrival order). We study two techniques, inspired by external sorting algorithms, to store data incrementally as it arrives, simultaneously providing good performance for recording and querying. We present concurrency control and recovery schemes for both techniques. We show the benefits of our techniques both analytically and experimentally.
Basiliximab: efficacy and safety evaluation in kidney transplantation

Introduction: Basiliximab is a chimeric monoclonal antibody directed against the alpha chain of interleukin-2 receptor (IL-2R). When administered intravenously at a dosage of 20 mg at the time of transplantation and 4 days later, basiliximab saturates the alpha chain of IL-2R for 4 weeks. Areas covered: This review evaluates the efficacy and safety of basiliximab in kidney transplantation. Randomized controlled trials showed that basiliximab can significantly reduce the incidence of acute rejection without increasing the risk of adverse events. When compared with other antibodies used for induction, basiliximab showed efficacy and safety profiles similar to daclizumab, another monoclonal antibody directed against the alpha chain of IL-2R. In comparison with rabbit anti-thymocyte globulins (rATG), basiliximab showed a similar efficacy. However, in patients at higher risk of rejection, rATG proved to be more effective. No serious safety problems related to basiliximab have been reported. Expert opinion: There is a solid evidence that basiliximab can significantly decrease the risk of acute rejection in kidney transplant recipients without increasing adverse events. This can allow decreased dosage or avoidance of glucocorticoids and reduced dosage of calcineurin inhibitors. On the basis of efficacy, tolerability, ease of administration, and cost effectiveness, basiliximab may be considered the drug of choice for the prophylaxis of acute rejection in standard renal transplant recipients.