Miracle-dz/UniFAR-FTUs huggingface dataset:
miR‐106a is frequently upregulated in gastric cancer and inhibits the extrinsic apoptotic pathway by targeting FAS

Emerging evidence has shown the association of aberrantly expressed miR‐106a with cancer development, however, little is known about its potential role in gastric carcinogenesis. In our present study, obviously overexpressed miR‐106a was found in gastric cancer tissues compared with their nontumor counterparts. Suppression of miR‐106a significantly inhibited gastric cancer cell proliferation and triggered apoptosis. Bioinformatic analysis combining with validation experiments identified FAS as a direct target of miR‐106a. Rescue experiments and examination of caspase‐8, PARP and caspase‐3 further approved that miR‐106a could inhibit gastric cancer cell apoptosis through interfering with FAS‐mediated apoptotic pathway. Moreover, a significant inverse correlation was found between miR‐106a and FAS expression not only in gastric cancer cell lines but also in gastric cancer specimens. Taken together, these findings suggest that ectopicly overexpressed miR‐106a may play an oncogenic role in gastric carcinogenesis and impair extrinsic apoptotic pathway through targeting FAS. © 2012 Wiley Periodicals, Inc.
Sex-Dependent Regulation of Aromatase-Mediated Synaptic Plasticity in the Basolateral Amygdala

The basolateral amygdala (BLA) integrates sensory input from cortical and subcortical regions, a function that requires marked synaptic plasticity. Here we provide evidence that cytochrome P450 aromatase (AROM), the enzyme converting testosterone to 17β-estradiol (E2), contributes to the regulation of this plasticity in a sex-specific manner. We show that AROM is expressed in the BLA, particularly in the basolateral nucleus (BL), in male and female rodents. Systemic administration of the AROM inhibitor letrozole reduced spine synapse density in the BL of adult female mice but not in the BL of male mice. Similarly, in organotypic corticoamygdalar slice cultures from immature rats, treatment with letrozole significantly reduced spine synapses in the BL only in cultures derived from females. In addition, letrozole sex-specifically altered synaptic properties in the BL: in acute slices from juvenile (prepubertal) female rats, wash-in of letrozole virtually abolished long-term potentiation (LTP), whereas it did not prevent the generation of LTP in the slices from males. Together, these data indicate that neuron-derived E2 modulates synaptic plasticity in rodent BLA sex-dependently. As protein expression levels of AROM, estrogen and androgen receptors did not differ between males and females and were not sex-specifically altered by letrozole, the findings suggest sex-specific mechanisms of E2 signaling. SIGNIFICANCE STATEMENT The basolateral amygdala (BLA) is a key structure of the fear circuit. This research reveals a sexually dimorphic regulation of synaptic plasticity in the BLA involving neuronal aromatase, which produces the neurosteroid 17β-estradiol (E2). As male and female neurons in rodent BLA responded differently to aromatase inhibition both in vivo and in vitro, our findings suggest that E2 signaling in BLA neurons is regulated sex-dependently, presumably via mechanisms that have been established during sexual determination. These findings could be relevant for the understanding of sex differences in mood disorders and of the side effects of cytochrome P450 aromatase inhibitors, which are frequently used for breast cancer therapy.
Fully automated esophagus segmentation with a hierarchical deep learning approach

Segmentation of organs at risk in CT volumes is a prerequisite for radiotherapy treatment planning. In this paper we focus on esophagus segmentation, a challenging problem since the walls of the esophagus have a very low contrast in CT images. Making use of Fully Convolutional Networks (FCN), we present several extensions that improve the performance, including a new architecture that allows to use low level features with high level information, effectively combining local and global information for improving the localization accuracy. Experiments demonstrate competitive performance on a dataset of 30 CT scans.
Measurement of affinity in serum samples of antigen‐free, germ‐free and conventional mice after hyperimmunization with 2,4‐dinitrophenyl keyhole limpet hemocyanin, using surface plasmon resonance

We previously investigated the primary and secondary responses and hyperimmunization to the T cell‐dependent antigen 2,4‐dinitrophenyl keyhole limpet hemocyanin (DNP‐KLH) in antigen‐free (AF), germ‐free (GF) and conventional (CV) mice. Both the absolute and relative numbers of DNP‐specific IgG‐secreting cells in the spleen of AF mice were considerably higher compared to GF and CV mice, especially after hyperimmunization. In the present study we measured the total and DNP‐specific IgG concentration in the sera of these hyperimmunized mice using a sensitive sandwich enzyme‐linked immunosorbent assay. With respect to the total IgG concentration before and after hyperimmunization, the AF mice showed an almost 13‐fold increase after boosting with the antigen; the GF mice showed an approximately 8‐fold increase. A slight but non‐significant increase was observed in the CV mice. The total as well as the DNP‐specific IgG levels in the AF‐immunized mice were 2‐fold and 5‐fold higher compared to GF and CV mice, respectively. With the use of Surface Plasmon Resonance instrumentation (BIAcoreTM, Pharmacia, Uppsala, Sweden) we obtained mean binding affinities (KA) of the polyclonal samples of the three groups of hyperimmunized mice. IgA and IgM samples displayed low affinity for DNP‐lysine. The AF mice displayed the highest KA value among IgG antibodies, followed by GF mice, while CV mice showed a 3‐fold lower KA compared to AF mice. These differences were mainly determined by the dissociation rate constant (kdiss), since no significant changes were observed in the association rate constant (kass). Furthermore, the sera of the CV mice have a lower percentage of high‐affinity antibodies compared to GF and AF mice. These results suggest that besides a higher overall binding affinity seen in AF mice, and to a lesser extent in GF mice, the relative contribution of high‐affinity IgG is greater in AF mice compared to CV mice.
Corneal Epithelial Thinning Profile Induced by Long-Term Wear of Hydrogel Lenses

Purpose. To characterize the epithelial thickness profile and study the effects of long-term wear of hydrogel lenses on this profile. Methods. A cross-sectional study was designed. Epithelial thickness was evaluated in 15 subjects who had worn one of two types of low oxygen transmissibility (Dk) hydrogel contact lenses for an average of 10 years (range, 7–16) and compared with a group of 18 control subjects who had never worn contact lenses. Epithelial thickness was measured at the center and at four mid-peripheral and four peripheral locations in the vertical and horizontal meridians of the cornea using a modified optical pachymeter. Results. Lens wearers had significantly thinner epithelium than controls [analysis of variance (ANOVA), p < 0.001] in the central (41 ± 7 &mgr;m versus 48 ± 5 &mgr;m), mid-peripheral (41 ± 7 &mgr;m versus 48 ± 7 &mgr;m), and peripheral (42 ± 9 &mgr;m versus 48 ± 6 &mgr;m) cornea. The extent of this difference ranged from 8.7% to 18.4% of the total epithelial thickness, was not associated with the duration of wear (ANOVA, p = 0.87, power = 0.05), and was significantly greater for the lower Dk contact lens type (ANOVA, p < 0.001). Topographical position did not have a significant effect on epithelial thickness (ANOVA, p > 0.13, power > 0.22). Conclusion. This study establishes that the epithelial thinning associated with hydrogel lens wear is topographically uniform. It also confirms that this effect is inversely related to lens oxygen transmissibility but does not appear to increase with longer duration of wear.
Cellular-telephone use and brain tumors.

BACKGROUND Concern has arisen that the use of hand-held cellular telephones might cause brain tumors. If such a risk does exist, the matter would be of considerable public health importance, given the rapid increase worldwide in the use of these devices. METHODS We examined the use of cellular telephones in a case-control study of intracranial tumors of the nervous system conducted between 1994 and 1998. We enrolled 782 patients through hospitals in Phoenix, Arizona; Boston; and Pittsburgh; 489 had histologically confirmed glioma, 197 had meningioma, and 96 had acoustic neuroma. The 799 controls were patients admitted to the same hospitals as the patients with brain tumors for a variety of nonmalignant conditions. RESULTS As compared with never, or very rarely, having used a cellular telephone, the relative risks associated with a cumulative use of a cellular telephone for more than 100 hours were 0.9 for glioma (95 percent confidence interval, 0.5 to 1.6), 0.7 for meningioma (95 percent confidence interval, 0.3 to 1.7), 1.4 for acoustic neuroma (95 percent confidence interval, 0.6 to 3.5), and 1.0 for all types of tumors combined (95 percent confidence interval, 0.6 to 1.5). There was no evidence that the risks were higher among persons who used cellular telephones for 60 or more minutes per day or regularly for five or more years. Tumors did not occur disproportionately often on the side of head on which the telephone was typically used. CONCLUSIONS These data do not support the hypothesis that the recent use of hand-held cellular telephones causes brain tumors, but they are not sufficient to evaluate the risks among long-term, heavy users and for potentially long induction periods.
Improving Decision Making at the End of Life With Video Images

Background. Decision making at the end of life is frequently complex and often filled with uncertainty. We hypothesized that people with limited health literacy would have more uncertainty about end-of-life decision making than people with adequate literacy. We also hypothesized that video images would decrease uncertainty. Design. Before and after oral survey. Participants. Subjects presenting to their primary care physicians. Methods. Subjects were asked about their preferences for end-of-life care after they heard a verbal description of advanced dementia and were asked to rate the level of their uncertainty. Subjects then viewed a video of a patient with advanced dementia and were asked again about their preferences and uncertainty. Uncertainty was measured using the Decisional Conflict Scale with score ranges from 3 (high uncertainty) to 15 (no uncertainty). Health literacy was measured using the Rapid Estimate of Adult Literacy in Medicine, and subjects were divided into 3 literacy categories: low (0—45, 6th grade and below), marginal (46— 60, 7th—8th grade), and adequate (61—66, 9th grade and above). Results. A total of 146 patients completed the interview. Prior to the video, the average uncertainty scores for subjects with low, marginal, and adequate health literacy were 10.8, 12.4, and 13.5, respectively (P < 0.0001). After the video, the 3 groups had similar uncertainty about their decisions. The average uncertainty scores for subjects with low, marginal, and adequate health literacy were 13.6, 14.1, and 14.5, respectively (P = 0.046). Conclusions. Subjects with limited health literacy expressed more uncertainty about their preferences for end-of-life care than did subjects with adequate literacy. Our video decision aid improved end-of-life decision making by decreasing uncertainty regarding subjects’ preferences, especially for those with limited literacy.
Follow-the-leader cell migration requires biased cell–cell contact and local microenvironmental signals

Directed cell migration often involves at least two types of cell motility that include multicellular streaming and chain migration. However, what is unclear is how cell contact dynamics and the distinct microenvironments through which cells travel influence the selection of one migratory mode or the other. The embryonic and highly invasive neural crest (NC) are an excellent model system to study this question since NC cells have been observed in vivo to display both of these types of cell motility. Here, we present data from tissue transplantation experiments in chick and in silico modeling that test our hypothesis that cell contact dynamics with each other and the microenvironment promote and sustain either multicellular stream or chain migration. We show that when premigratory cranial NC cells (at the pre-otic level) are transplanted into a more caudal region in the head (at the post-otic level), cells alter their characteristic stream behavior and migrate in chains. Similarly, post-otic NC cells migrate in streams after transplantation into the pre-otic hindbrain, suggesting that local microenvironmental signals dictate the mode of NC cell migration. Simulations of an agent-based model (ABM) that integrates the NC cell behavioral data predict that chain migration critically depends on the interplay of biased cell–cell contact and local microenvironment signals. Together, this integrated modeling and experimental approach suggests new experiments and offers a powerful tool to examine mechanisms that underlie complex cell migration patterns.
Adaptive Host-Abandonment of Ectoparasites Before Fledging? Within-Brood Distribution of Nest Mites in House Sparrow Broods

We studied the within-brood distribution of a haematophagous mite Pellonyssus reedi living on nestling house sparrows (Passer domesticus) near the time of fledging. We measured the natural level of infestation of individual nestlings, and determined the feeding efficiency of mites, by scoring their feeding status. Within-brood distribution of mite loads was unrelated to nestling body mass, tarsus length, or immunocompetence. These results did not support parasite preference for large or susceptible hosts. Mite feeding-efficiency was also unrelated to these nestling characteristics, confirming that large nestlings or nestlings with less-developed immunocompetence did not provide superior feeding conditions for mites. Therefore, our results do not support the hypothesis that within-brood distribution of avian ectoparasites is explained by the parasites' preferences for characteristics, such as large body size or low immunocompetence, that make nestlings suitable hosts. On the other hand, we found that mite loads were negatively correlated with nestling age and feather length, suggesting that nestlings closer to fledging harbored fewer mites then their less-developed nestmates. Furthermore, feather length had a stronger relationship with parasite distribution than did nestling age. We presume, therefore, that feather characteristics, i.e., length, may serve as a signal for mites to perceive the ready-to-fledge state of nestlings, inducing abandonment behavior. These results support another, largely neglected hypothesis, i.e., that the avoidance or abandonment of those nestlings that are close to fledging may also explain the parasites' distribution in a brood. This hypothesis is based on the argument that many nest-dwelling ectoparasites breed in the nest material and emerge only periodically to feed on nestlings. In such parasites, the ability to recognize and avoid mature fledglings can be adaptive because this may help the parasites to avoid their removal from the nest so they can continue to reproduce by feeding on unfledged chicks of the current or later broods. Our results suggest that adaptive host-abandonment by nest-dwelling ectoparasites can influence within-brood parasite distributions around the time of fledging.
Medial Medullary Infarction Identified by Diffusion-Weighted Magnetic Resonance Imaging

Objective: To elucidate the frequency and clinical profiles of patients with medial medullary infarction (MMI) identified by diffusion-weighted MRI (DWI). Methods: We assessed the frequency, radiological findings, etiology and clinical features of MMI detected by DWI from our single-center registry of acute ischemic patients. Results: Thirty patients (1.5% of 2,014 with ischemic stroke) had MMI, including isolated unilateral MMI in 26 patients. Lesions were located by DWI in the rostral medulla of 25 patients (83%). Culprit infarcts that were undetectable by DWI in 6 (38%) of 16 patients who were assessed within 24 h after onset were later confirmed as MMI. The major etiological mechanism was small artery occlusion (SAO; 19 patients) and the median initial National Institutes of Health Stroke Scale score was 4 (interquartile range: 3–4.75). The most frequent symptom was contralateral hemiparesis (27 patients). None of the patients fulfilled the classical Dejerine Triad. Twenty-two patients (73%) had a modified Rankin Scale score of ≤2 at 3 months. A patient developed transient ischemic attack within 3 months; none developed recurrent stroke. Conclusions: Rostral medullary infarction with mild neurological deficits resulting from SAO is relatively frequent. Because emergency DWI within 24 h could not detect MMI in one third of the patients, this type of infarction could be misdiagnosed as capsular/pontine lacunae or other neurological disorders.
Low Molecular Weight Trypsin-Plasmin Inhibitors Isolated from Papain Treated Urinary Trypsin Inhibitor

Summary Papain treatment of human urinary trypsin inhibitor (UTI67; mol. wt. 43,000 by SDS-polyacrylamide gel electrophoresis, specific activity 1,897 U/mg protein) produced four new protease inhibitors, which were highly purified by gel chromatography on Sephadex G-100 and isoelectric focusing. The purified inhibitors (UTI26, UTI9-I, UTI9-II, and UTI9-III) were shown to be homogeneous by polyacrylamide disc gel electrophoresis, and had apparent molecular weights of 26,000, 9,000, 9,000, and 9,800, respectively, by sodium dodecyl sulfate gel electrophoresis. During enzymatic degradation of UTI67, the amino acid compositions changed to more basic, and the isoelectric point increased from pH 2.0 (UTI67) to pHs 4.4, 5.2, 6.6, and 8.3 (UTI26, UTI9-I, UTI9-II, and UTI9-III), respectively. Both the parent and degraded inhibitors had anti-plasmin activity as well as antitrypsin and anti-chymotrypsin activities. Much higher anti-plasmin/anti-trypsin and anti-plasmin/anti-chymotrypsin activities were observed in the degraded inhibitors than in the parent UTI67. They competitively inhibited human plasmin with Ki values of 1.13 X 10-7 - 2.12 X 10-6 M (H-D-Val-Leu-Lys-pNA substrate). The reactions were very fast and the active site of the inhibitors to plasmin was thought to be different from that to trypsin or chymotrypsin.
Contributions of O Island 48 to Adherence of Enterohemorrhagic Escherichia coli O157:H7 to Epithelial Cells In Vitro and in Ligated Pig Ileal Loops

ABSTRACT O island 48 (OI-48) of Escherichia coli consists of three functional gene clusters that encode urease, tellurite resistance (Ter), and putative adhesins Iha and AIDA-1. The functions of these clusters in enterohemorrhagic E. coli (EHEC) O157:H7 infection are unknown. Deletion mutants for these three regions were constructed and evaluated for their ability to adhere to epithelial cells in vitro and in ligated pig ileal loops. Deletion of the Ter gene cluster reduced the ability of the organism to adhere to and form large clusters on IPEC-J2 and HEp-2 cells. Complementation of the mutation by introducing the wild-type ter genes restored adherence and large-cluster formation. Tests in ligated pig ileal loops showed a decrease in colonization by the Ter-negative mutant, but the difference was not significant compared to colonization by the wild type (26.4% ± 21.2% versus 40.1% ± 19.1%; P = 0.168). The OI-48 aidA gene deletion had no effect on adherence in vitro or in vivo. Deletion of the iha and ureC genes had no effect on adherence in vitro but significantly reduced the colonization of EHEC O157:H7 in the ligated pig intestine. These data suggest that Ter, Iha, and urease may contribute to EHEC O157:H7 pathogenesis by promoting adherence of the pathogen to the host intestinal epithelium.
Which electroencephalography (EEG) for epilepsy? The relative usefulness of different EEG protocols in patients with possible epilepsy

Background and aim: Electroencephalography (EEG) is an essential investigative tool for use in young people with epilepsy. This study assesses the effects of different EEG protocols on the yield of EEG abnormalities in young people with possible new epilepsy. Methods: 85 patients presenting to the unit underwent three EEGs with differing protocols: routine EEG (r-EEG), sleep-deprived EEG (SD-EEG), EEG carried out during drug-induced sleep (DI-EEG). The yield of EEG abnormalities was compared using each EEG protocol. Results: 98 patients were recruited to the study. Of the 85 patients who completed the study, 33 (39%) showed no discernible abnormality on any of their EEG recordings. 36 patients (43%) showed generalised spike and wave during at least one EEG recording, whereas 15 (18%) had a focal discharge evident at some stage. SD-EEG had a sensitivity of 92% among these patients, whereas the sensitivity of DI-EEG and r-EEG was 58% and 44%, respectively. The difference between the yield from SD-EEG was significantly higher than that from other protocols (p<0.001). Among the 15 patients showing focal discharges, SD-EEG provoked abnormalities in 11 (73%). r-EEG and DI-EEG each produced abnormalities in 40% and 27%, respectively. 7 patients (47%) had changes seen only after sleep deprivation. In 2 (13%), the only abnormalities were seen on r-EEG. In only 1 patient with focal discharges (7%) was the focal change noted solely after drug-induced sleep. These differences did not reach significance. Conclusion: EEG has an important role in the classification of epilepsies. SD-EEG is an easy and inexpensive way of increasing the yield of EEG abnormalities. Using this as the preferred protocol may help reduce the numbers of EEGs carried out in young patients presenting with epilepsy.
Experience from teaching performance analysis of object-oriented systems

This paper reports our experience from teaching "Performance Analysis of Object-Oriented Systems" which was offered for the first time in the spring of 2004. The class was designed for juniors/seniors and graduate students majoring in Computer Science and Computer Engineering. The main focus of this course is on the implementations of class loading, Just-In-Time compiler, threading, and garbage collection in virtual machines supporting Object-Oriented languages such as Java and C#. We adopted Microsoft Shared Source Common Language Infrastructure (SSCLI) as the main experimental platform and the "Shared Source CLI Essentials" as one of the main accompanying textbooks. We find that the combination of SSCLI and the book provides a very effective means to deliver the course contents. In this paper, a complete documentation of the course design, the evaluation of students' work, and the instructor's reflection is presented