Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effect of Stereoscopic Immersive Environments on Projection-Based Multi-dimensional Data Visualization

Multidimensional data impose a challenge for visual analyses. Commonly, dimensionality reduction techniques are used to project the multidimensional data into a 2D visual space. Poco et al. [9] showed that projection into a 3D visual space can increase the performance of common visual analysis tasks due to a higher projection precision. They also backed up their findings with a user study. However, when conducting the user study they displayed the 3D visual space on a 2D screen, which may impede the correct perception of the third dimension. In this paper, we present a study that investigates the effect of stereoscopic environments when used for the visual analysis of multidimensional data after projection into a 3D visual space. We conducted a controlled user study to compare correctness, timing, and confidence in segregation and precision tasks when performed in stereoscopic immersive environments and on a nonstereoscopic 2D screen. In terms of the stereoscopic immersive environments, we operated on and compared results obtained with two setup: a single screen and a six-sided highly immersive system, in both of which interaction was performed with a 3D input device. We investigated whether the stereoscopic immersive environments have an effect on user performance depending on the visual encodings. We used both 3D scatter plots and cluster visualizations in the form of enclosing surfaces or hulls for the visual analysis tasks.
Hypovitaminosis D in dogs with spirocercosis.

BACKGROUND Spirocercosis in dogs is characterized by esophageal nodules that can undergo neoplastic transformation. Hypovitaminosis D has been associated with neoplasia formation. We hypothesized hypovitaminosis D in neoplastic spirocercosis and that it could be a risk factor for neoplastic transformation. OBJECTIVE To measure and compare vitamin D status, assessed by serum 25-hydroxyvitamin D [25(OH)D] concentrations in non-neoplastic (n = 25) and neoplastic (n = 26) spirocercosis client-owned dogs and healthy dogs (n = 24). ANIMALS Twenty-five non-neoplastic dogs, 26 neoplastic dogs, and 24 healthy dogs. METHODS Fifty-one dogs were randomly selected from 119 dogs diagnosed with spirocercosis presenting to our hospital, and further divided into non-neoplastic or neoplastic groups. Exclusion criteria included dogs less than 1 year old, with concurrent diseases, received corticosteroids, or treated prophylactically for spirocercosis. Serum 25(OH)D concentration was measured by high-performance liquid chromatography. Spirocercosis dogs' appetites were graded and compared. RESULTS Serum 25(OH)D concentrations were significantly different among all groups (P < .001). 25-Hydroxyvitamin D concentrations were significantly lower in neoplastic group (median 30.7 nmol/L [range 14.7-62.2]) compared to non-neoplastic (median 52.7 nmol/L [range 19.1-129.7, P < .05]) and healthy groups (median 74.6 nmol/L [range 37.4-130.5, P < .005]). 25-hydroxyvitamin D concentrations were significantly lower in non-neoplastic spirocercosis dogs compared to healthy ones (P < .05). Neoplastic and non-neoplastic spirocercosis dogs had similar appetite scores (P = 1.0). 25-Hydroxyvitamin D concentrations were not significantly different between dogs with normal (P = .087) and abnormal (P = .125) appetites within neoplastic and non-neoplastic spirocercosis groups. CONCLUSIONS AND CLINICAL IMPORTANCE Further studies are warranted to determine potential use of vitamin D treatment in spirocercosis and explore role of hypovitaminosis D in pathogenesis of malignant transformation.
Inhibiting farnesylation of progerin prevents the characteristic nuclear blebbing of Hutchinson-Gilford progeria syndrome.

Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disorder that is characterized by dramatic premature aging and accelerated cardiovascular disease. HGPS is almost always caused by a de novo point mutation in the lamin A gene (LMNA) that activates a cryptic splice donor site, producing a truncated mutant protein termed "progerin. " WT prelamin A is anchored to the nuclear envelope by a farnesyl isoprenoid lipid. Cleavage of the terminal 15 aa and the farnesyl group releases mature lamin A from this tether. In contrast, this cleavage site is deleted in progerin. We hypothesized that retention of the farnesyl group causes progerin to become permanently anchored in the nuclear membrane, disrupting proper nuclear scaffolding and causing the characteristic nuclear blebbing seen in HGPS cells. Also, we hypothesized that blocking farnesylation would decrease progerin toxicity. To test this hypothesis, the terminal CSIM sequence in progerin was mutated to SSIM, a sequence that cannot be farnesylated. SSIM progerin relocalized from the nuclear periphery into nucleoplasmic aggregates and produced no nuclear blebbing. Also, blocking farnesylation of authentic progerin in transiently transfected HeLa, HEK 293, and NIH 3T3 cells with farnesyltransferase inhibitors (FTIs) restored normal nuclear architecture. Last, treatment of both early- and late-passage human HGPS fibroblasts with FTIs resulted in significant reductions in nuclear blebbing. Our results suggest that treatment with FTIs represents a potential therapy for patients with HGPS.
Understanding FRET as a Research Tool for Cellular Studies

Communication of molecular species through dynamic association and/or dissociation at various cellular sites governs biological functions. Understanding these physiological processes require delineation of molecular events occurring at the level of individual complexes in a living cell. Among the few non-invasive approaches with nanometer resolution are methods based on Förster Resonance Energy Transfer (FRET). FRET is effective at a distance of 1–10 nm which is equivalent to the size of macromolecules, thus providing an unprecedented level of detail on molecular interactions. The emergence of fluorescent proteins and SNAP- and CLIP- tag proteins provided FRET with the capability to monitor changes in a molecular complex in real-time making it possible to establish the functional significance of the studied molecules in a native environment. Now, FRET is widely used in biological sciences, including the field of proteomics, signal transduction, diagnostics and drug development to address questions almost unimaginable with biochemical methods and conventional microscopies. However, the underlying physics of FRET often scares biologists. Therefore, in this review, our goal is to introduce FRET to non-physicists in a lucid manner. We will also discuss our contributions to various FRET methodologies based on microscopy and flow cytometry, while describing its application for determining the molecular heterogeneity of the plasma membrane in various cell types.
Complications of Proton Pump Inhibitor Therapy.

Safety issues associated with proton pump inhibitors (PPIs) have recently attracted widespread media and lay attention. Gastroenterologists are frequently asked about the appropriateness of PPI therapy for specific patients. Furthermore, some patients may have had PPI therapy discontinued abruptly or inappropriately due to safety concerns. Faced with such a wide variety of potentially serious adverse consequences, prescribers need to evaluate the evidence objectively to discern the likelihood that any reported association might actually be causal. Here, we review many of the proposed adverse consequences of PPI therapy and apply established criteria for the determination of causation. We also consider the potential contribution of residual confounding in many of the reported studies. Evidence is inadequate to establish causal relationships between PPI therapy and many of the proposed associations. Residual confounding related to study design and the overextrapolation of quantitatively small estimates of effect size have probably led to much of the current controversy about PPI safety. In turn, this has caused unnecessary concern among patients and prescribers. The benefits of PPI therapy for appropriate indications need to be considered, along with the likelihood of the proposed risks. Patients with a proven indication for a PPI should continue to receive it in the lowest effective dose. PPI dose escalation and continued chronic therapy in those unresponsive to initial empiric therapy is discouraged.
Iterative Deepening Dynamic Time Warping for Time Series

Time series are a ubiquitous form of data occurring in virtually every scientific discipline and business application. There has been much recent work on adapting data mining algorithms to time series databases. For example, Das et al. attempt to show how association rules can be learned from time series [7]. Debregeas and Hebrail [8] demonstrate a technique for scaling up time series clustering algorithms to massive datasets. Keogh and Pazzani introduced a new, scalable time series classification algorithm [16]. Almost all algorithms that operate on time series data need to compute the similarity between them. Euclidean distance, or some extension or modification thereof, is typically used. However as we will demonstrate in Section 2.1, Euclidean distance can be an extremely brittle distance measure.
A Rice Stowaway MITE for Gene Transfer in Yeast

Miniature inverted repeat transposable elements (MITEs) lack protein coding capacity and often share very limited sequence similarity with potential autonomous elements. Their capability of efficient transposition and dramatic amplification led to the proposition that MITEs are an untapped rich source of materials for transposable element (TE) based genetic tools. To test the concept of using MITE sequence in gene transfer, a rice Stowaway MITE previously shown to excise efficiently in yeast was engineered to carry cargo genes (neo and gfp) for delivery into the budding yeast genome. Efficient excision of the cargo gene cassettes was observed even though the excision frequency generally decreases with the increase of the cargo sizes. Excised elements insert into new genomic loci efficiently, with about 65% of the obtained insertion sites located in genes. Elements at the primary insertion sites can be remobilized, frequently resulting in copy number increase of the element. Surprisingly, the orientation of a cargo gene (neo) on a construct bearing dual reporter genes (gfp and neo) was found to have a dramatic effect on transposition frequency. These results demonstrated the concept that MITE sequences can be useful in engineering genetic tools to deliver cargo genes into eukaryotic genomes.
The pinocytic rate of activated macrophages

Peritoneal macrophages from mice injected 4 days previously with Brewer's thioglycollate medium have a pinocytic rate, in culture, of 190 ng horseradish peroxidase (HRP)/100 mug cell protein/h, compared to the rate of resident peritoneal cells of 53 ng HRP/100 mug cell protein/h. Mice injected with endotoxin or with only certain of the components of the Brewer's medium show an intermediate level of stimulation. The rate of unstimulated, endotoxin-stimulated, or thioglycollate-stimulated cells shows little change over several days in culture. The pinocytic rate of thioglycollate-stimulated cells can, however, be further increased by exposure of concanavalin A. Although cells may show transient increases in their pinocytic rate in many situations, a sustained increase in pinocytic rate is a sign of the "activated" state of macrophages.
AMPK-dependent Repression of Hepatic Gluconeogenesis via Disruption of CREB·CRTC2 Complex by Orphan Nuclear Receptor Small Heterodimer Partner*

Orphan nuclear receptor small heterodimer partner (SHP) plays a key role in transcriptional repression of gluconeogenic enzyme gene expression. Here, we show that SHP inhibited protein kinase A-mediated transcriptional activity of cAMP-response element-binding protein (CREB), a major regulator of glucose metabolism, to modulate hepatic gluconeogenic gene expression. Deletion analysis of phosphoenolpyruvate carboxykinase (PEPCK) promoter demonstrated that SHP inhibited forskolin-mediated induction of PEPCK gene transcription via inhibition of CREB transcriptional activity. In vivo imaging demonstrated that SHP inhibited CREB-regulated transcription coactivator 2 (CRTC2)-mediated cAMP-response element-driven promoter activity. Furthermore, overexpression of SHP using adenovirus SHP decreased CRTC2-dependent elevations in blood glucose levels and PEPCK or glucose-6-phosphatase (G6Pase) expression in mice. SHP and CREB physically interacted and were co-localized in vivo. Importantly, SHP inhibited both wild type CRTC2 and S171A (constitutively active form of CRTC2) coactivator activity and disrupted CRTC2 recruitment on the PEPCK gene promoter. In addition, metformin or overexpression of a constitutively active form of AMPK (Ad-CA-AMPK) inhibited S171A-mediated PEPCK and G6Pase gene expression, and hepatic glucose production and knockdown of SHP partially relieved the metformin- and Ad-CA-AMPK-mediated repression of hepatic gluconeogenic enzyme gene expression in primary rat hepatocytes. In conclusion, our results suggest that a delayed effect of metformin-mediated induction of SHP gene expression inhibits CREB-dependent hepatic gluconeogenesis.
Proteome Profile of Starch Granules Purified from Rice (Oryza sativa) Endosperm

Starch is the most important food energy source in cereals. Many of the known enzymes involved in starch biosynthesis are partially or entirely granule-associated in the endosperm. Studying the proteome of rice starch granules is critical for us to further understand the mechanisms underlying starch biosynthesis and packaging of starch granules in rice amyloplasts, consequently for the improvement of rice grain quality. In this article, we developed a protocol to purify starch granules from mature rice endosperm and verified the quality of purified starch granules by microscopy observations, I2 staining, and Western blot analyses. In addition, we found the phenol extraction method was superior to Tris-HCl buffer extraction method with respect to the efficiency in recovery of starch granule associated proteins. LC-MS/MS analysis showed identification of already known starch granule associated proteins with high confidence. Several proteins reported to be involved in starch synthesis in prior genetic studies in plants were also shown to be enriched with starch granules, either directly or indirectly, in our studies. In addition, our results suggested that a few additional candidate proteins may also be involved in starch synthesis. Furthermore, our results indicated that some starch synthesis pathway proteins are subject to protein acetylation modification. GO analysis and KEGG pathway enrichment analysis showed that the identified proteins were mainly located in plastids and involved in carbohydrate metabolism. This study substantially advances the understanding of the starch granule associated proteome in rice and post translational regulation of some starch granule associated proteins.
Experimental pneumococcal meningitis: role of leukocytes in pathogenesis

Two groups of rabbits with experimental meningitis induced by direct intracisternal inoculation of Streptococcus pneumoniae cells were studied. One group was rendered profoundly leukopenic by nitrogen mustard, and the other had normal leukocyte counts. The two groups had comparable bacterial growth rates (mean generation time, 60 versus 67 min) and ultimate bacterial populations in the cerebrospinal fluid (CSF) (mean log10 CFU, 9.1 versus 8.7); therefore leukocytes did not effectively slow or limit the growth of pneumococci in the CSF in vivo. Increased CSF protein, decreased CSF glucose, and increased CSF lactate levels were similar in both groups, suggesting that leukocytes are not essential for these changes to occur. Quantitative blood cultures revealed identical levels of pneumococcal bacteremia until 13 to 14 h after the initiation of infection, when the leukopenic rabbits showed a larger number of pneumococci in the blood, ultimately exceeding the number reached in nonleukopenic rabbits by 100-fold. Leukocytes therefore limit the extent of pneumococcal bacteremia after infection of the CSF despite their lack of effect on the course or the CSF manifestations of experimental meningitis.
An introduction to the reading of Bion

The author suggests that a good deal of the confusion that arises in the course of reading Bion derives from the fact that Bion's analytic writing is comprised of two periods of work that involve markedly different conceptions of psychoanalysis. These two periods require of the reader very different ways of reading and generate contrasting experiences in reading. Bion, in passages in Learning from experience (1962) and Attention and interpretation (1970), offers advice to the reader regarding how he would like his ‘early’ and ‘late’ work to be read. The author treats the experience of reading these passages as ports of entry into the fundamental tenets underlying Bion's widely differing conceptions of the psychoanalytic enterprise. The experience of reading early Bion generates a sense of psychoanalysis as a never completed process of clarifying obscurities and obscuring clarifications, which enterprise moves in the direction of a convergence of disparate meanings. Incontrast, the experience of reading Bion's later work conveys a sense of psychoanalysis as a process involving a movement toward infinite expansion of meaning. The author offers a detailed account of an analytic experience which he discusses from a point of view informed by Bion's work, particularly his late work.
Risk Factors for Tuberculosis

The risk of progression from exposure to the tuberculosis bacilli to the development of active disease is a two-stage process governed by both exogenous and endogenous risk factors. Exogenous factors play a key role in accentuating the progression from exposure to infection among which the bacillary load in the sputum and the proximity of an individual to an infectious TB case are key factors. Similarly endogenous factors lead in progression from infection to active TB disease. Along with well-established risk factors (such as human immunodeficiency virus (HIV), malnutrition, and young age), emerging variables such as diabetes, indoor air pollution, alcohol, use of immunosuppressive drugs, and tobacco smoke play a significant role at both the individual and population level. Socioeconomic and behavioral factors are also shown to increase the susceptibility to infection. Specific groups such as health care workers and indigenous population are also at an increased risk of TB infection and disease. This paper summarizes these factors along with health system issues such as the effects of delay in diagnosis of TB in the transmission of the bacilli.
Temporal Coding in Pavlovian Conditioning: Hall-Pearce Negative Transfer

The Hall-Pearce (1979) negative transfer effect in rats was used to examine whether temporal relationships are coded as part of the informational content of associations that result from CS-US pairings. The transfer effect consists of adeficit in conditioned responding following CS-USstrong pairings in Phase 2 that results from prior CS-USweak pairings in Phase 1. Using conditioned bar-press suppression, we found that gaps of different duration between CS termination and US onset in the two training phases resulted in less of a Hall-Pearce negative transfer effect than did an equivalent gap in the twotraining phases. The results are discussed with respect tothe temporal coding hypothesis (Matzel, Held, & Miller, 1988), the Pearce and Hall (1980) model, and Bouton's (1993) interference model.
Biochar from Sugarcane Filtercake Reduces Soil CO2 Emissions Relative to Raw Residue and Improves Water Retention and Nutrient Availability in a Highly-Weathered Tropical Soil

In Brazil, the degradation of nutrient-poor Ferralsols limits productivity and drives agricultural expansion into pristine areas. However, returning agricultural residues to the soil in a stabilized form may offer opportunities for maintaining or improving soil quality, even under conditions that typically promote carbon loss. We examined the use of biochar made from filtercake (a byproduct of sugarcane processing) on the physicochemical properties of a cultivated tropical soil. Filtercake was pyrolyzed at 575°C for 3 h yielding a biochar with increased surface area and porosity compared to the raw filtercake. Filtercake biochar was primarily composed of aromatic carbon, with some residual cellulose and hemicellulose. In a three-week laboratory incubation, CO2 effluxes from a highly weathered Ferralsol soil amended with 5% biochar (dry weight, d.w.) were roughly four-fold higher than the soil-only control, but 23-fold lower than CO2 effluxes from soil amended with 5% (d.w.) raw filtercake. We also applied vinasse, a carbon-rich liquid waste from bioethanol production typically utilized as a fertilizer on sugarcane soils, to filtercake- and biochar-amended soils. Total CO2 efflux from the biochar-amended soil in response to vinasse application was only 5% of the efflux when vinasse was applied to soil amended with raw filtercake. Furthermore, mixtures of 5 or 10% biochar (d.w.) in this highly weathered tropical soil significantly increased water retention within the plant-available range and also improved nutrient availability. Accordingly, application of sugarcane filtercake as biochar, with or without vinasse application, may better satisfy soil management objectives than filtercake applied to soils in its raw form, and may help to build soil carbon stocks in sugarcane-cultivating regions.
TEMPORAL LOBE EPILEPSY

Seventy‐four patients with temporal lobe epilepsy, resistant to medication, who in 1960–1969 underwent unilateral temporal lobe resection at Rigshospitalet, Copenhagen. In only 12 patients was no etiological factor found. In three‐quarters of the patients a peri‐ or postnatal injury was the suspected etiology of the epilepsy; and in one‐third, a history of complications in the actual and/or abnormal outcome of a previous pregnancy was recorded. Only seven patients had experienced febrile convulsions. Patients with certain combinations of etiological factors, including encephalitis, have a poor prognosis regarding relief from seizures. Patients in whom an abnormal outcome of the mother's previous pregnancies is recorded have a poor prognosis as regards psychiatric normalization. Apart from this no correlation has been found between the surgical results and the numbers or types of the various etiological factors.
Acceptance of apparel private sale sites by consumers: application of original and extended technology acceptance model

In this study, the private sale sites, a new way of online retailing of especially fashion type of apparel products, are investigated in order to determine and understand the acceptance of them by the consumers. The factors that determine the attitude and intention of consumers toward private sale sites are analyzed using two models: the original technology acceptance model (TAM) and proposed TAM which is extended with addition of distinctive features of these sites. These features are specified as quality dimensions in three groups, namely, system flexibility, service reputation, and service attractiveness. Both TAM and proposed TAM models are validated using confirmatory factor analysis and structural equation modeling on the data obtained from a sample of 344 people living in Turkey. In the end, it is suggested that the apparel retailers to focus on the service attractiveness and service reputation in order to influence the attitude of the consumers and motivate them to use the private sale sites.