Miracle-dz/UniFAR-FTUs huggingface dataset:
How to explain the discordant change of ulcerative colitis and Crohn disease in adjacent or even the same regions and time periods.

T o the Editor: I read with great interest the article by Malmborg et al (1) regarding the increase of ulcerative colitis (UC) but decrease in Crohn disease (CD) in children in northern Stockholm County during 2005–2007 after a previous decade-long continuous increase in CD and stability of UC. This article also discussed the discordances in the incidence, ratio, and temporal changes of UC versus CD in other Scandinavian and Western countries over time (2–5). It remains a big puzzle and seems overwhelmingly complex; however, in my opinion, it could be extremely simple. Most of these studies are in children, which may rule out many presently suspected factors such as smoking. Recently, I came up with a unified hypothesis for the etiology of inflammatory bowel disease (IBD) (6), suggesting that UC and CD may be just 2 manifestations of the same morbidity rather than 2 different diseases. Both UC and CD may be caused by the inhibition of gut bacteria by some dietary chemicals and the resultant overdigestion of the mucus layer and gut tissue by poorly inactivated proteases. Although I focus on saccharin and sucralose in my article (6), other dietary chemicals such as cyclamate and acesulfame K actually have similar inhibitory effects on gut bacteria as saccharin, thus may also be linked to IBD (7). According to the proposed hypothesis, certain extent inhibition of gut bacteria by a factor may cause UC, whereas a further inhibition by even the same factor may lead to a shift toward CD (6). Thus, the simultaneous increase in UC but decrease in CD in northern Stockholm as shown in the study by Malmborg et al may be caused by a decreased exposure of some causative factor such as a remarkable decrease in cyclamate consumption because of a change in European Union regulation in 2004 that reduced the maximum permitted level for cyclamate in soft drinks from 400 to 250 mg/L (8,9). Interestingly, in 2004, the European Union approved the marketing of sucralose, which is suspected to be linked to IBD (6). Cyclamate is heavily used in countries such as Denmark (8,9) and Sweden (10), with consumption far beyond the acceptable daily intake in some children, whereas the use of cyclamate in the neighboring Norway is near zero (11); however, a study conducted in 2007 found high concentrations of sucralose in the surface water near cities such as Oslo, Norway, but much lower concentrations in cities in Sweden and Denmark (12). The negligible use of cyclamate but heavy use of sucralose in Norway is in accordance with the remarkable increase in pediatric IBD in southeastern Norway during 2005–2007 (3). We can see that the differences in legislation and marketing in food additives makes it possible for big variations among different regions and over time. Thus, the peculiar pattern of changes may not be that mysterious and it may have actually reflected the innate similarity and connection between UC and CD, rather than the differences between them. Xiaofa Qin Department of Surgery, UMDNJ-New Jersey Medical School, Newark
A robust detection and isolation scheme for abrupt and incipient faults in nonlinear systems

This paper presents a robust fault diagnosis scheme for abrupt and incipient faults in nonlinear uncertain dynamic systems. A detection and approximation estimator is used for online health monitoring. Once a fault is detected, a bank of isolation estimators is activated for the purpose of fault isolation. A key design issue of the proposed fault isolation scheme is the adaptive residual threshold associated with each isolation estimator. A fault that has occurred can be isolated if the residual associated with the matched isolation estimator remains below its corresponding adaptive threshold, whereas at least one of the components of the residuals associated with all the other estimators exceeds its threshold at some finite time. Based on the class of nonlinear uncertain systems under consideration, an isolation decision scheme is devised and fault isolability conditions are given, characterizing the class of nonlinear faults that are isolable by the robust fault isolation scheme. The nonconservativeness of the fault isolability conditions is illustrated by deriving a subclass of nonlinear systems and of faults for which these conditions are also necessary for fault isolability. Moreover, the analysis of the proposed fault isolation scheme provides rigorous analytical results concerning the fault isolation time. Two simulation examples are given to show the effectiveness of the fault diagnosis methodology.
Chronic hyponatremia reduces survival of magnocellular vasopressin and oxytocin neurons after axonal injury

Axonal injury to hypothalamic magnocellular vasopressin (AVP) and oxytocin (OT) neurons causes degeneration of a substantial subpopulation of these neurons. In this study, we investigated the influence of osmolality on this injury-induced cell death. Normonatremic, chronically hypernatremic, and chronically hyponatremic rats received pituitary stalk compression (SC), which causes degeneration of AVP and OT terminals in the neurohypophysis. Twenty-one days after SC, rats were perfused and hypothalami were serially sectioned and alternately stained for AVP-neurophysin and OT- neurophysin immunoreactivities. Normonatremic and hypernatremic rats exhibited a triphasic pattern of water intake after SC, with peak intakes 3 times higher than those exhibited by sham-operated normonatremic rats. In contrast, hyponatremic SC rats exhibited peak water intakes of 600 ml/24 hr, approximately 9–10 times the water intakes of sham-operated normonatremic rats. In normonatremic rats, SC caused degeneration of 65% of the AVP neuron population in the SON and 73% in the PVN, but only 31% of the OT neuron population in the SON and 35% in the PVN. Similar results were found in hypernatremic rats after SC. However, in hyponatremic rats SC caused degeneration of 97% of the AVP neuron population in the SON and 93% in the PVN, and 90% of the OT neuron population in the SON and 84% in the PVN. Our results, therefore, demonstrate that injury-induced degeneration of magnocellular AVP and OT neurons is markedly exacerbated by chronic hypo-osmolar conditions, but neuronal survival is not enhanced by chronic hyperosmolar conditions.
Transgenerational epigenetic effects of the Apobec1 cytidine deaminase deficiency on testicular germ cell tumor susceptibility and embryonic viability

Environmental agents and genetic variants can induce heritable epigenetic changes that affect phenotypic variation and disease risk in many species. These transgenerational effects challenge conventional understanding about the modes and mechanisms of inheritance, but their molecular basis is poorly understood. The Deadend1 (Dnd1) gene enhances susceptibility to testicular germ cell tumors (TGCTs) in mice, in part by interacting epigenetically with other TGCT modifier genes in previous generations. Sequence homology to A1cf, the RNA-binding subunit of the ApoB editing complex, raises the possibility that the function of Dnd1 is related to Apobec1 activity as a cytidine deaminase. We conducted a series of experiments with a genetically engineered deficiency of Apobec1 on the TGCT-susceptible 129/Sv inbred background to determine whether dosage of Apobec1 modifies susceptibility, either alone or in combination with Dnd1, and either in a conventional or a transgenerational manner. In the paternal germ-lineage, Apobec1 deficiency significantly increased susceptibility among heterozygous but not wild-type male offspring, without subsequent transgenerational effects, showing that increased TGCT risk resulting from partial loss of Apobec1 function is inherited in a conventional manner. By contrast, partial deficiency in the maternal germ-lineage led to suppression of TGCTs in both partially and fully deficient males and significantly reduced TGCT risk in a transgenerational manner among wild-type offspring. These heritable epigenetic changes persisted for multiple generations and were fully reversed after consecutive crosses through the alternative germ-lineage. These results suggest that Apobec1 plays a central role in controlling TGCT susceptibility in both a conventional and a transgenerational manner.
Farmers Market Locations and Their Determinants: An Empirical Analysis in New England

After a strong expansion across the United States, farmers markets’ (FMs) growth rate has declined in spite of policymakers’ interest in promoting them. In this study we model farmers’ participation in FMs and investigate what market factors affect FMs’ location using zip-code-level data for the New England states. Our results suggest that market size, education, presence of children in the household and SNAP participation lend to the establishment of FMs, more than income per se. Farming activities has a positive association with the likelihood of FMs, while proxies for establishment costs and the presence of traditional distribution channels may play a limiting role in their formation.
Yoga, its health benefits, and the search for the true self

by COLLEEN M. MCCOY (Under the Direction of Su-I Hou) ABSTRACT The purpose of this study is to explore the lived experience of yoga practitioners, and their search for the true self. The research questions guiding this study were: 1) How does a yoga practitioner describe the concept of the true self? 2) How does a yoga practitioner describe the experience of the true self while engaged in a yoga practice? 3) How does a yoga practitioner describe the experience of the true self in everyday life? I interviewed three yoga practitioners for this qualitative study. The participants were purposively chosen. Heideggerian phenomenology was the method employed to examine the lived experience of the true self. The overall themes that emerged from the data include 1) the value of yoga, 2) the body as a vehicle for the self, 3) relationships, 4) the self versus the true self, and 5) transformation.
Shc proteins are strong, independent prognostic markers for both node-negative and node-positive primary breast cancer.

Activated Shc signaling proteins are implicated in many pathways associated with aggressive disease, and many breast cancer cell lines derived from highly aggressive tumors contain high levels of activated, tyrosine phosphorylated (PY)-Shc (the M(r) 46000 and M(r) 52000 isoforms) relative to levels of an inhibitory M(r) 66000 Shc isoform. It was, therefore, hypothesized that high amounts of PY-Shc relative to the M(r) 66000 Shc isoform would serve as a marker for aggressive neoplasms. Semiquantitative immunohistochemical analyses of PY-Shc and p66 Shc were performed on archival primary breast tumor specimens from 116 women, 17 of whom experienced relapse (6.1 years median follow-up of nonrelapsed patients). Consistent with our hypothesis, staining intensities demonstrated that increased amounts of PY-Shc (P = 0.01) and decreased expression of p66-Shc protein (P = 0.028) correlated with disease recurrence. Modeled as the ratio of PY-Shc to p66 Shc, the Shc ratio correlated strongly with nodal status (P = 0.003), tumor stage (P = 0.0025), and disease stage (P = 0.002) and was 2-fold higher in primary tumors of patients who subsequently relapsed (P < 0.001). Univariate Cox proportional hazards analysis of relapse-free survival demonstrated the prognostic value of PY-Shc (P = 0.01), p66 Shc (P = 0.04), and the Shc ratio (P = 0.004) as continuous variables, with a hazard ratio (HR) of 10 (P = 0.007) for the Shc ratio. Shc ratio cut points of <0.35 and >0.65 were identified and independently validated to maximize negative predictive value and positive predictive value. Patients with low Shc ratios (n = 36) had a 0.08 HR of relapse (P = 0.007) compared with patients with high Shc ratios, experiencing an 8-year cumulative 2.9% and 55% relapse hazard, respectively, compared with a 22% relapse hazard in the total cohort. The Shc ratio had similar prognostic value for disease-specific survival. In multivariate models, the Shc ratio, both as a continuous variable and as a cut point-categorized variable, was independent of all measured covariates (including nodal status, tumor stage, disease stage, grade, estrogen receptor status, and adjuvant therapy) and was a stronger prognostic marker than all but nodal status. All relapsed node-positive patients had very high Shc ratios (>0.80; P = 0.006) in their primary tumors. Furthermore, the Shc ratio was a strong, independent prognostic indicator in node-negative patients (79 patients, 10 recurrences), with a HR of 0.086 (P = 0.02) that was independent of clinical markers and adjuvant therapy. Patients with low and high Shc ratios experienced a 3.6% and 64% relapse hazard, respectively, compared with 20% in the total node-negative cohort.
Losing the stem-loop structure from metazoan mitochondrial tRNAs and co-evolution of interacting factors

Conventional tRNAs have highly conserved sequences, four-armed cloverleaf secondary structures, and L-shaped tertiary structures. However, metazoan mitochondrial tRNAs contain several exceptional structures. Almost all tRNAsSer for AGY/N codons lack the D-arm. Furthermore, in some nematodes, no four-armed cloverleaf-type tRNAs are present: two tRNAsSer without the D-arm and 20 tRNAs without the T-arm are found. Previously, we showed that in nematode mitochondria, an extra elongation factor Tu (EF-Tu) has evolved to support interaction with tRNAs lacking the T-arm, which interact with C-terminal domain 3 in conventional EF-Tu. Recent mitochondrial genome analyses have suggested that in metazoan lineages other than nematodes, tRNAs without the T-arm are present. Furthermore, even more simplified tRNAs are predicted in some lineages. In this review, we discuss mitochondrial tRNAs with divergent structures, as well as protein factors, including EF-Tu, that support the function of truncated metazoan mitochondrial tRNAs.
Acoustic Cues in the Directionality of Stop Consonant Confusions

Acoustic cues in the directionality of stop consonant confusions by Madelaine Claire Plauche B.S. (University of Texas, Austin) 1995 M.A. (University of California, Berkeley) 1997 A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Linguistics in the GRADUATE DIVISION of the UNIVERSITY OF CALIFORNIA, BERKELEY Committee in charge: Professor John Ohala, Chair Professor Ian Maddieson Doctor Elizabeth Shriberg Professor Nelson Morgan Fall 2001 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission.
Language Development and the Ontogeny of the Dorsal Pathway

In the absence of clear phylogenetic data on the neurobiological basis of the evolution of language, comparative studies across species and across ontogenetic stages within humans may inform us about the possible neural prerequisites of language. In the adult human brain, language-relevant regions located in the frontal and temporal cortex are connected via different fiber tracts: ventral and dorsal pathways. Ontogenetically, it has been shown that newborns display an adult-like ventral pathway at birth. The dorsal pathway, however, seems to display two subparts which mature at different rates: one part, connecting the temporal cortex to the premotor cortex, is present at birth, whereas the other part, connecting the temporal cortex to Broca’s area, develops much later and is still not fully matured at the age of seven. At this age, typically developing children still have problems in processing syntactically complex sentences. We therefore suggest that the mastery of complex syntax, which is at the core of human language, crucially depends on the full maturation of the fiber connection between the temporal cortex and Broca’s area.
User Acceptance of Emergency Alert Technology : A Case Study

The purpose of the study is to investigate the factors affecting the user acceptance of emergency alert systems. By studying the adoption of a SMS-based alert system at a large public university in the United States, this paper explores the research question: How are different motivational factors related to the intention and behavior of using emergency alert technology? Through a mixed-methods approach, the study demonstrates a “deepening” effort in applying the technology acceptance model (TAM) to emergency response system, drawing attention to the holistic nature of motivation-behavior in technology acceptance. Results of this research show that: the concept of usefulness has multiple levels of meanings to its intended users; the ease of use is more about the users’ ability to control the system behavior; and subjective norm need to be examined with relation to its originating source.
SMSnet: Semantic motion segmentation using deep convolutional neural networks

Interpreting the semantics and motion of objects are prerequisites for autonomous robots that enable them to reason and operate in dynamic real-world environments. Existing approaches that tackle the problem of semantic motion segmentation consist of long multistage pipelines and typically require several seconds to process each frame. In this paper, we present a novel convolutional neural network architecture that learns to predict both the object label and motion status of each pixel in an image. Given a pair of consecutive images, the network learns to fuse features from self-generated optical flow maps and semantic segmentation kernels to yield pixel-wise semantic motion labels. We also introduce the Cityscapes-Motion dataset which contains over 2,900 manually annotated semantic motion labels, which is the largest dataset of its kind so far. We demonstrate that our network outperforms existing approaches achieving state-of-the-art performance on the KITTI dataset, as well as in the more challenging Cityscapes-Motion dataset while being substantially faster than existing techniques.
Heterogeneity in electrical activity of the canine ileal circular muscle: interaction of two pacemakers

Abstract In cross‐sectioned slabs from the muscularis externa or in the isolated circular muscle devoid of longitudinal muscle and myenteric plexus (MyP) of ileum, a slow wave, sigmoidal or triangular in shape, was recorded from microelectrode impalements near the deep muscular plexus (DMP) region in the whole‐thickness preparation. From the MyP region of whole‐thickness preparations, a slow wave which oscillated at a similar frequency (9–10 cycles min−1) was characterized by a fast upstroke and a square shape. Slow waves of μmixed pattern were recorded in the outer circular muscle (OCM) while triangular slow waves were present near the submucous plexus (SMP). In this preparation but not in isolated circular muscle, the inhibitory junction potentials (IJPs) produced by supramaximal electrical field stimulation triggered slow waves. The amplitudes (15–25 mV) of spontaneous and triggered slow waves (TSWs) were greatest in the MyP region, significantly so compared to those of DMP and SMP regions and to those in all regions of isolated circular muscle. Frequencies of slow waves recorded from the MyP and DMP were slightly but significantly higher than those recorded from either the OCM or the SMP or from all regions of isolated circular muscle. A 10–15 mV gradient in resting membrane potential (more hyperpolarized near MyP) existed across the intact (but not the isolated) circular muscle layer. Both types of slow waves, TSWs and IJPs were unaffected by muscarinic, adrenergic or tachykinergic blockade. We suggest that a MyP pacemaker network generated a plateau‐type slow wave while a DMP one induced a triangular slow wave. Each source can function independently but the MyP network may dominate and entrain DMP slow waves.
Clinically Relevant Antibiotic Resistance Mechanisms Can Enhance the In Vivo Fitness of Neisseria gonorrhoeae

In 2007 the Centers for Disease Control and Prevention placed Neisseria gonorrhoeae on the infamous “Super Bugs” list to highlight the high prevalence of strains resistant to relatively inexpensive antibiotics, such as penicillin, tetracycline and fluoroquinolones, previously used in therapy to treat gonorrhea (Shafer et al., 2010). This event was significant because the gonococcus, a strict human pathogen, causes > 95 million infections worldwide each year and since the mid-1940s mankind has relied on effective antibiotic therapy to treat infections and stop local spread of disease. Today, such therapy is threatened by antibiotic resistance. Specifically, the third generation cephalosporins, especially ceftriaxone, may be losing their effectiveness since some (albeit still rare) isolates in the Far East, most recently Japan, and Europe have displayed clinical resistance to currently used levels of ceftriaxone, and treatment failures have been reported (Ohnishi et al., 2011; Unemo et al., 2010). Concern has been raised that the spectrum of resistance expressed by some gonococcal strains may make standard antibiotic treatment for gonorrhea ineffective in the not too distant future (Dionne-Odom et al., 2011). Without new, effective antibiotics or novel combination therapies of existing antibiotics, the reproductive health of the world’s sexually active population may be placed at risk due to such antibiotic resistant gonococci.
Undocumented Latina Immigrants in Orange County, California: A Comparative Analysis 1

This article examines a unique data set randomly collected from Latinas (including 160 undocumented immigrants) and non-Hispanic white women in Orange County, California, including undocumented and documented Latina immigrants, Latina citizens, and non-Hispanic white women. Our survey suggests that undocumented Latinas are younger than documented Latinas, and immigrant Latinas are generally younger than U.S.-citizen Latinas and Anglo women. Undocumented and documented Latinas work in menial service sector jobs, often in domestic services. Most do not have job-related benefits such as medical insurance. Despite low incomes and likelihood of having children under age 18 living with them, their use of public assistance was low. Undocumented and documented Latina immigrants lived in households that often contained extended family members; they were more likely than other women in the study to lack a regular source of health care, to utilize health clinics, public health centers, and hospital emergency rooms rather than private physicians or HMOs, and to underutilize preventative cancer screening services. Despite their immigration status, undocumented Latina immigrants often viewed themselves as part of a community in the United States, which significantly influenced their intentions to stay in the United States. Contrary to much of the recent public policy debate over immigration, we did not find that social services influenced Latina immigrants’ intentions to stay in the United States.