Miracle-dz/UniFAR-FTUs huggingface dataset:
CD44 splicing pattern is associated with disease progression in pulmonary adenocarcinoma.

BACKGROUND AND PURPOSE Certain alternatively spliced exons of CD44 gene have been associated with specific functions. However, these functions may have come from inclusion of a central array of alternatively spliced exons, rather than a single one. The goals of this study were to analyze all of the variant exons included by alternative splicing, the entire population of CD44 mRNA transcripts, and the prognostic implications of CD44 mRNA and protein isoforms expressed by non-small cell lung cancer (NSCLC). METHODS Using a polymerase chain reaction protocol with short reaction times, we amplified, sequenced and quantified CD44 mRNA transcripts from 52 samples of NSCLC to determine the splicing patterns of alternatively included exons and the proportion of each CD44 mRNA transcript. The expression of CD44 standard form and variant isoforms CD44v3 and CD44v6 were also analyzed by immunohistochemistry (IHC). RESULTS Normal lung and NSCLC expressed CD44 mRNA transcripts containing variant exons v10, v8-10, v6-10, v3-10 and v2-10. In squamous cell carcinoma, the expression rates of these mRNA transcripts were equal to or higher than those of the normal lung, and the splicing pattern was not associated with disease progression. In adenocarcinoma, the expression rates of CD44v6-10, v3-10 and v2-10 mRNA were lower than in normal lung. The down-regulation of CD44v6-10, CD44v3-10 mRNA and CD44v6 protein paralleled the progression of adenocarcinoma. Recurrence of adenocarcinoma was associated with negative expression of CD44v6-10 or CD44v3-10 mRNA, and with low-level expression of CD44v6 or CD44v3 by IHC. Negative expression of CD44v6-10 mRNA and reduced expression of CD44 v6 protein were associated with a shorter disease-free and overall survival in the univariate but not the multivariate analysis. CONCLUSION Our data suggest that CD44 splicing pattern is associated with disease progression in adenocarcinoma.
A Tubular Biomaterial Construct Exhibiting a Negative Poisson’s Ratio

Developing functional small-diameter vascular grafts is an important objective in tissue engineering research. In this study, we address the problem of compliance mismatch by designing and developing a 3D tubular construct that has a negative Poisson’s ratio νxy (NPR). NPR constructs have the unique ability to expand transversely when pulled axially, thereby resulting in a highly-compliant tubular construct. In this work, we used projection stereolithography to 3D-print a planar NPR sheet composed of photosensitive poly(ethylene) glycol diacrylate biomaterial. We used a step-lithography exposure and a stitch process to scale up the projection printing process, and used the cut-missing rib unit design to develop a centimeter-scale NPR sheet, which was rolled up to form a tubular construct. The constructs had Poisson’s ratios of -0.6 ≤ νxy ≤ -0.1. The NPR construct also supports higher cellular adhesion than does the construct that has positive νxy. Our NPR design offers a significant advance in the development of highly-compliant vascular grafts.
HLA antigen distribution in renal transplant recipients and donors.

BACKGROUND HLA typing analysis is important in renal transplant patient. This study is the first report from Nepal to find out distribution of HLA A, B, DR antigen in live related renal transplant recipients and donors from Nepal. The aim of this study was to investigate the distribution of HLA in the live related renal transplant recipients and donors of Nepal. METHODS In a retrospective study, HLA patterns were defined in 100 live related renal transplant recipients and donors. One year study is done from June 2011 to May 2012. The study was done by using sequence specific oligonucleotides primers and polymerase chain reaction and assay. Allele frequencies were obtained by direct counting. RESULTS A total of 12 HLA-A, 15 HLA-B and 13 HLA-DRB1 alleles were identified at the four-digit level in the live related renal transplant recipients and donors of Nepal. High frequency alleles were HLA-A*11 (34.5%), A*24 (17%), A*33 (13%); HLA-B*15(27%), B*35(19%), B*40 (10%); HLA-DRB1*15 (33.5%), DRB1*12 (21.4%) and DRB1*04 (7.32%). CONCLUSIONS These results showed considerable heterogeneity in both HLA class I and class II antigens. To reduce the risk of allograft rejection, transplantation from HLA matched donors is recommended.
Comparative study of Misgav-Ladach and Pfannenstiel-Kerr cesarean techniques: a randomized controlled trial

Aim. To compare Pfannenstiel-Kerr (PKM) and Misgav-Ladach (MLM) methods in terms of operation-related features and neonatal outcome in primary cesarean deliveries. Methods. A total of 180 pregnant women randomized into PKM (n = 90) or MLM (n = 90) groups were included in this study. Primary outcome measures were total operative and extraction times, Apgar score, blood loss, wound complications, and the suture use. Secondary outcome measures were wound seroma and infection incidence, time of bowel restitution, and the perceived pain. Results. Total operation and extraction times were significantly shorter and less suture material was used in the MLM group than the PKM group (p < 0.001). Initially, higher scores obtained for 6 h-VAS in the MLM group (p < 0.05) were normalized after 24 h of the operation. PKM and MLM were similar in terms of preoperative and postoperative levels of hemoglobin and hematocrit, wound complication, bowel restitution, fever, seroma, infection, wound dehiscence and the need for transfusion, antibiotic, and analgesics. Conclusion. The operation-related morbidity of the MLM and PKM for primary C/S seem to be comparable; however, the MLM seems to be superior in terms of operation time and the amount of suture usage but inferior in pain scores in the early postoperative period.
A static simulation of dynamic delimited control

We present a continuation-passing-style (CPS) transformation for some dynamic delimited-control operators, including Felleisen’s control and prompt, that extends a standard call-by-value CPS transformation. Based on this new transformation, we show how Danvy and Filinski’s static delimited-control operators shift and reset simulate dynamic operators, allaying in passing some skepticism in the literature about the existence of such a simulation. The new CPS transformation and simulation use recursive delimited continuations to avoid undelimited control and the overhead it incurs in implementation and reasoning.
Role of the RNA-Binding Protein IMP-2 in Muscle Cell Motility

ABSTRACT Insulin-like growth factor 2 (IGF-2) mRNA-binding proteins (IMPs) are a family of posttranscriptional regulatory factors with well-understood roles in embryonic development and cancer but with poorly characterized functions in normal adult cells and tissues. We now show that IMP-2, the most ubiquitously expressed member of the family, is abundant in human and mouse adult skeletal myoblasts, where it is indispensable for cell motility and for stabilization of microtubules. To explore the functions of IMP-2, we analyzed the transcripts that were differentially regulated in IMP-2-depleted myoblasts and bound to IMP-2 in normal myoblasts. Among them were the mRNAs of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein. By gain- and loss-of-function assays and gel shift experiments, we show that IMP-2 regulates the expression of PINCH-2 and MURF-3 proteins via direct binding to their mRNAs. Upregulation of PINCH-2 in IMP-2-depleted myoblasts is the key event responsible for their decreased motility. Our data reveal how the posttranscriptional regulation of gene expression by IMP-2 contributes to the control of adhesion structures and stable microtubules and demonstrate an important function for IMP-2 in cellular motility.
Timing of GA4/7 application and the flowering of Pinus sylvestris grafts in the greenhouse.

Effects of varying the time of stem injection of gibberellin A4/7 (GA4/7) on male and female flowering in potted grafts of Pinus sylvestris L. in a greenhouse were monitored in two consecutive years. Flowering results for each application time were correlated with phenological characteristics and abiotic factors in an attempt to find reproducible indicators of the most effective time of GA4/7 treatment. The GA4/7 treatment had a significant effect on female flowering, but no effect on male flowering. In both years, the largest effect on female flowering was obtained with the latest application. Percent shoot and needle elongation (relative to final length) were poor indicators of the optimal time of GA4/7 application. Three heat sum accumulation models gave equally accurate predictions of the optimal time for GA4/7 application; therefore, the simplest model, i.e., the sum of degree-days, is recommended. The timing window for stimulation of female flowering with GA4/7 had a lower limit of about 500 degree-days (threshold +5 degrees C), and the optimal time of GA4/7 application was after about 700 degree-days.
Neurologic and neuroimaging manifestations of Cantú syndrome

Objective: To describe the neurologic and neuroimaging manifestations associated with Cantú syndrome. Methods: We evaluated 10 patients with genetically confirmed Cantú syndrome. All adult patients, and pediatric patients who were able to cooperate and complete the studies, underwent neuroimaging, including vascular imaging. A salient neurologic history and examination was obtained for all patients. Results: We observed diffusely dilated and tortuous cerebral blood vessels in all patients who underwent vascular imaging. White matter changes were observed in all patients who completed an MRI brain study. Two patients had a persistent trigeminal artery. One patient had an occluded right middle cerebral artery. One patient had transient white matter changes suggestive of posterior reversible encephalopathic syndrome. Four patients had migraines with one patient having complicated migraines. Seizures were seen in early life but infrequent. The majority of patients had mild developmental delays and one patient had a diagnosis of autism. Conclusions: Cantú syndrome is associated with various neurologic manifestations, particularly cerebrovascular findings including dilated and tortuous cerebral vessels, white matter changes, and persistent fetal circulation. Involvement of the KATP SUR2/Kir6.1 subtype potentially plays an important role in the neurologic manifestations of Cantú syndrome.
Mathematical and Kinetic Modelling for Convective Hot Air Drying of Sweet Potatoes ( Ipomoea batatas L )

The kinetic modelling of thin layer drying is performed with various agricultural products such as seeds, grains, fruits and some plant species with economic importance. Sweet Potato (Ipomoea batatas L) is a widely consumed, and its industrialization is on the increase. The thin layer drying kinetics of sweet potato were experimentally investigated in a convective hot air dryer. Comparison was made between the experimental and model predicted moisture ratio by nonlinear regression analysis. Furthermore, the effect of drying temperature and slice thickness on the selected model constants was evaluated. From the experimental data obtained, it was observed that moisture ratio of the potato sample was directly proportional to the mass of the sample while the time of drying was inversely proportional and these two parameters (mass and time) were used to develop a mathematical model for the thin layer drying of sweet potatoes using a convective hot air dryer. The mathematical model developed was validated. The experimental data fitted the developed mathematical model and gave the Sum of Squares (SSE) value of 0.0001296 and coefficient of determination (R2) as unity. The parameters obtained from the kinetic modelling of the selected models studied could be used in designing low cost dryers for optimum drying conditions.
Acetylene in breath: background levels and real-time elimination kinetics after smoking

We have measured the acetylene concentration in the exhaled breath of 40 volunteers (31 non-smokers, nine smokers) using near-infrared cavity ring-down spectroscopy. The acetylene levels were found to be the same as in ambient air for non-smokers, whereas elevated levels were observed for smokers. Real-time measurements with sub-second time resolution have been applied to measure the elimination kinetics of acetylene in breath after exposure to tobacco smoke. Three exponential time constants can be distinguished from the data and these can be used to define the residence times for different compartments, according to the multi-compartment model of the human body.
Hubs of brain functional networks are radically reorganized in comatose patients

Human brain networks have topological properties in common with many other complex systems, prompting the following question: what aspects of brain network organization are critical for distinctive functional properties of the brain, such as consciousness? To address this question, we used graph theoretical methods to explore brain network topology in resting state functional MRI data acquired from 17 patients with severely impaired consciousness and 20 healthy volunteers. We found that many global network properties were conserved in comatose patients. Specifically, there was no significant abnormality of global efficiency, clustering, small-worldness, modularity, or degree distribution in the patient group. However, in every patient, we found evidence for a radical reorganization of high degree or highly efficient “hub” nodes. Cortical regions that were hubs of healthy brain networks had typically become nonhubs of comatose brain networks and vice versa. These results indicate that global topological properties of complex brain networks may be homeostatically conserved under extremely different clinical conditions and that consciousness likely depends on the anatomical location of hub nodes in human brain networks.
Parkin overexpression during aging reduces proteotoxicity, alters mitochondrial dynamics, and extends lifespan

Aberrant protein aggregation and mitochondrial dysfunction have each been linked to aging and a number of age-onset neurodegenerative disorders, including Parkinson disease. Loss-of-function mutations in parkin, an E3 ubiquitin ligase that functions to promote the ubiquitin–proteasome system of protein degradation and also in mitochondrial quality control, have been implicated in heritable forms of Parkinson disease. The question of whether parkin can modulate aging or positively impact longevity, however, has not been addressed. Here, we show that ubiquitous or neuron-specific up-regulation of Parkin, in adult Drosophila melanogaster, increases both mean and maximum lifespan without reducing reproductive output, physical activity, or food intake. Long-lived Parkin-overexpressing flies display an increase in K48-linked polyubiquitin and reduced levels of protein aggregation during aging. Recent evidence suggests that Parkin interacts with the mitochondrial fission/fusion machinery to mediate the turnover of dysfunctional mitochondria. However, the relationships between parkin gene activity, mitochondrial dynamics, and aging have not been explored. We show that the mitochondrial fusion-promoting factor Drosophila Mitofusin, a Parkin substrate, increases in abundance during aging. Parkin overexpression results in reduced Drosophila Mitofusin levels in aging flies, with concomitant changes in mitochondrial morphology and an increase in mitochondrial activity. Together, these findings reveal roles for Parkin in modulating organismal aging and provide insight into the molecular mechanisms linking aging to neurodegeneration.
Prognostic impact of the CD34+/CD38− cell burden in patients with acute myeloid leukemia receiving allogeneic stem cell transplantation

In acute myeloid leukemia (AML), leukemia‐initiating cells exist within the CD34+/CD38− cell compartment. They are assumed to be more resistant to chemotherapy, enriched in minimal residual disease cell populations, and responsible for relapse. Here we evaluated clinical and biological associations and the prognostic impact of a high diagnostic CD34+/CD38− cell burden in 169 AML patients receiving an allogeneic stem cell transplantation in complete remission. Here, the therapeutic approach is mainly based on immunological graft‐versus‐leukemia effects. Percentage of bone marrow CD34+/CD38− cell burden at diagnosis was measured using flow cytometry and was highly variable (median 0.5%, range 0%–89% of all mononuclear cells). A high CD34+/CD38− cell burden at diagnosis associated with worse genetic risk and secondary AML. Patients with a high CD34+/CD38− cell burden had shorter relapse‐free and overall survival which may be mediated by residual leukemia‐initiating cells in the CD34+/CD38− cell population, escaping the graft‐versus‐leukemia effect after allogeneic transplantation. Evaluating the CD34+/CD38− cell burden at diagnosis may help to identify patients at high risk of relapse after allogeneic transplantation. Further studies to understand leukemia‐initiating cell biology and develop targeting therapies to improve outcomes of AML patients are needed.
Digital imaging fluorescence microscopy: spatial heterogeneity of photobleaching rate constants in individual cells

Photobleaching and related photochemical processes are recognized experimental barriers to quantification of fluorescence by microscopy. We have measured the kinetics of photobleaching of fluorophores in living and fixed cells and in microemulsions, and have demonstrated the spatial variability of these processes within individual cells. An inverted fluorescence microscope and a high-sensitivity camera, together with high-speed data acquisition by a computer-controlled image processor, have been used to control precisely exposure time to excitation light and to record images. To improve the signal-to-noise ratio, 32 digital images were integrated. After correction for spatial variations in camera sensitivity and background fluorescence, the images of the relative fluorescence intensities for 0.065 micron2 areas in the object plane were obtained. To evaluate photobleaching objectively, an algorithm was developed to fit a three-parameter exponential equation to 20 images recorded from the same microscope field as a function of illumination time. The results of this analysis demonstrated that the photobleaching process followed first-order reaction kinetics with rate constants that were spatially heterogeneous and varied, within the same cell, between 2- and 65-fold, depending on the fluorophore. The photobleaching rate constants increased proportionally with increasing excitation intensity and, for benzo(a)pyrene, were independent of probe concentration over three orders of magnitude (1.25 microM to 1.25 mM). The propensity to photobleach was different with each fluorophore. Under the cellular conditions used in these studies, the average rates of photobleaching decreased in this order: N-(7-nitrobenz-2-oxa-1,3-diazole)-23,24-dinor- 5-cholen-22-amine-3 beta-ol greater than acridine orange greater than rhodamine-123 greater than benzo(a)pyrene greater than fluorescein greater than tetramethylrhodamine greater than 1,1'dioctadecyl- 3,3,3',3'-tetramethylindocarbocyanine. The photobleaching appears to be an oxidation reaction, in that the addition of saturated solutions of Na2S2O5 to mineral oil microemulsions eliminated photobleaching of N-(7- nitrobenz-2-oxa-1,3-diazole)-23,24-dinor-5-cholen-22-amine-3 beta-ol or benzo(a)pyrene. We identified experimental conditions to observe, without detectable photobleaching, fluorophores in living cells, which can not be studied anaerobically. Useful images were obtained when excitation light was reduced to eliminate photobleaching, as determined from zero-time images calculated from the exponential fit routine. (ABSTRACT TRUNCATED AT 400 WORDS)
Probing the neurophysiology of anxiety: Social stress alters the modulation of serotonin neurons

Anxiety disorders are prevalent in human and veterinary medicine yet the underlying mechanism is poorly understood. Because serotonin (5-HT) neurons of the dorsal raphe (DR) are thought to play a prominent role, my goal was to understand the changes in DR 5-HT neurons that underlie anxiety and other stressrelated disorders. Two DR subdivisions were studied in a series of experiments: the ventromedial DR (vmDR), a well characterized subfield with a high density of 5-HT neurons, and the lateral wing DR (lwDR), a largely uncharacterized subfield with a more sparse distribution of 5-HT neurons. Many stress paradigms activate 5-HT neurons of the lwDR more so than 5-HT neurons of the vmDR, suggesting a unique role for lwDR 5-HT cells in stress circuits. However, it is not known if lwDR 5-HT neurons possess physiological characteristics that contribute to their increased propensity to be activated by a stressor. I found that lwDR 5-HT neurons demonstrated increased intrinsic excitability, increased glutamatergic input, and similar GABAergic input when compared to vmDR 5-HT neurons. Using the chronic social defeat model of anxiety, the distinctions between lwDR and vmDR neurons were explored further. Social defeat induced anxious behavior and stress-associated pathological changes in the peripheral organs of intruder mice. For the first time, investigation into the neural mechanisms of social defeat has focused on 5-HT neuron physiology, revealing subregion-specific effects within the DR. Increased excitability was seen in the vmDR neurons of the most anxious mice. This was accompanied by a decrease in GABAergic input to vmDR 5-HT neurons potentially mediated by both presynaptic and postsynaptic changes. The lwDR 5-HT neurons demonstrated distinct stress-induced changes limited to the slower kinetics of postsynaptic GABAAR. The differential effect of social stress on inhibitory input to vmDR or lwDR neurons suggest that the 5-HT output in brain regions targeted by each subfield is differentially affected in anxiety disorders. Collectively these findings help fill the gap in our understanding of local DR circuitry, the heterogeneity of 5-HT neurons, and the distinct regulation of vmDR and lwDR neurons in the circuits that mediate stress and contribute to the pathophysiology of anxiety. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Neuroscience First Advisor Sheryl G. Beck
Two Novel Src Homology 2 Domain Proteins Interact to Regulate Dictyostelium Gene Expression during Growth and Early Development*

There are 13 Dictyostelium Src homology 2 (SH2) domain proteins, almost 10-fold fewer than in mammals, and only three are functionally unassigned. One of these, LrrB, contains a novel combination of protein interaction domains: an SH2 domain and a leucine-rich repeat domain. Growth and early development appear normal in the mutant, but expression profiling reveals that three genes active at these stages are greatly underexpressed: the ttdA metallohydrolase, the abcG10 small molecule transporter, and the cinB esterase. In contrast, the multigene family encoding the lectin discoidin 1 is overexpressed in the disruptant strain. LrrB binds to 14-3-3 protein, and the level of binding is highest during growth and decreases during early development. Comparative tandem affinity purification tagging shows that LrrB also interacts, via its SH2 domain and in a tyrosine phosphorylation-dependent manner, with two novel proteins: CldA and CldB. Both of these proteins contain a Clu domain, a >200-amino acid sequence present within highly conserved eukaryotic proteins required for correct mitochondrial dispersal. A functional interaction of LrrB with CldA is supported by the fact that a cldA disruptant mutant also underexpresses ttdA, abcG10, and cinB. Significantly, CldA is itself one of the three functionally unassigned SH2 domain proteins. Thus, just as in metazoa, but on a vastly reduced numerical scale, an interacting network of SH2 domain proteins regulates specific Dictyostelium gene expression.