Miracle-dz/UniFAR-FTUs huggingface dataset:
Integration of electrodeposited PdNi alloys with silicon and carbon nanotube electronics

This thesis investigates the electrodeposition of PdNi films with controllable composition and their suitability as electrical contacts in electronic and spintronic devices based on Silicon and Carbon nanotubes (CNTs). The electrodeposition process and characterisation of the electrical and magnetic properties of the deposited PdNi films are described. PdNi films with a wide composition range can be deposited from the same bath by changing the deposition potential. Electrical characterisation shows the formation of high quality PdNi-Si Schottky barriers while magnetic measurements prove the ferromagnetic nature of the PdNi films. Electrodeposited PdNi films are thus shown to be suitable contacts for electronic and spintronic devices. Hydrogen sensors comprising back to back electrodeposited PdNi-Si Schottky barriers are fabricated and characterised. The back to back architecture ensures low current operation at all biases. Palladium causes the Hydrogen molecules to dissociate and be absorbed by the film, while Nickel makes the sensor resistant to repeated cycling in the Hydrogen environment. The sensors exhibit extremely low idle currents, large percentage current increases on Hydrogen exposure and high selectivity for Hydrogen. These factors, in addition to the simplicity of fabrication and easy integration with conventional electronics show that electrodeposited PdNi-Si Schottky barriers are well suited for use as Hydrogen sensors. The workfunction change in PdNi films exposed to Hydrogen is used to characterise CNTs contacted by electrodeposited PdNi. The PdNi contacted CNTs exhibit ohmic characteristics, which change on exposure to Hydrogen. Examining this change allows differentiation between semiconducting and metallic CNTs. Raman spectroscopy is used to characterise the same CNTs and the results are compared with the electrical characterisation in Hydrogen. The electrical and Raman analysis experimentally verify the theoretically assigned CNT Raman features. The fabrication and electrical characterisation of CNT transistors incorporating electrodeposited PdNi contacts are presented. The CNTs are spin coated from a 1,2-dichlorobenzene dispersion and contacted with electrodeposited PdNi. The PdNi-Si Schottky barrier is used to suppress the current through the Silicon substrate during electrical characterisation. The operating restrictions imposed by the direct PdNi-Si contact and methods to overcome the same are discussed. The characteristics of the CNT transistor in a changing magnetic field at room temperature are presented.
Temporal regulation of Cre recombinase activity in neural stem cells

Neural stem cells are known to give rise to distinct subtypes of neurons and glial cells over time by changing their competency. However, precise characterization of neural stem cells at various developmental stages remains to be performed. For such analysis, a tool to manipulate neural stem cells at different time points is necessary. Here, we generated transgenic mice that express Cre‐ERT2 in the ventricular zone of the developing nervous system under the control of the nestin promoter and enhancer (Nes‐CreERT2). In mice expressing Cre‐ERT2 at appropriate levels, Cre recombinase activity was mostly inactive but efficiently activated by tamoxifen within 1 day. When such mice were crossed with the ROSA‐26 or Z/EG reporter mice, neural stem cells were permanently labeled after administration of tamoxifen. Thus, Nes‐CreERT2 mice offer a powerful tool to manipulate neural stem cells genetically at desired time points. genesis 44:233–238, 2006. © 2006 Wiley‐Liss, Inc.
Proliferative Nodules in Congenital Melanocytic Nevi: A Clinicopathologic and Immunohistochemical Analysis

Congenital melanocytic nevi (CMN) occur in 1% to 2% of newborns, and the risk of malignant melanoma is increased in patients with large CMN. Appearance at birth or later of a nodular or hyperpigmented area within a CMN simulates malignant melanoma and prompts biopsy. Although their clinical and pathologic features seem ominous, proliferative nodules (PNs) typically are benign and may regress, although atypical features cause greater concern. Here we report clinical and pathologic findings with outcome in 10 children who had multiple biopsies of large CMN with PNs. We reviewed 78 separate samples from the 10 patients and classified the 60 PNs according to published criteria. A subset of 30 samples containing both the CMN and a PNs was analyzed for immunohistochemical reactivity for melanocytic (S-100 protein, HMB45, melan-A), lymphocytic (CD45), cell-cycle/proliferative (Mib-1, p16, p21, p27, c-Myc), apoptotic (p53, Bax, c-kit, CD95), and anti-apoptotic (bcl-2) markers. Both CMN and PNs had similar expression of melanocytic, lymphocytic, and most cell-cycle/proliferative and apoptotic markers, including Mib-1, p16, p21, p27, c-Myc, Bax, CD95, and bcl-2. A greater proportion of PNs than CMN were reactive for p53 (67% vs. 30%, P < 0.0098) and c-kit (97% vs. 3%, P < 0.0001). p53 and p21 expression in CMN and all types of PNs were inversely correlated. When ordinary and atypical PNs were compared, the atypical PNs more frequently expressed p53, Mib-1, Bax, and bcl-2, but less frequently expressed p21. The c-kit expression in nearly all PNs and its absence in nearly all CMN is potentially useful for recognition of PN, suggests a delayed melanocytic maturation process in proliferative nodules, and may be likely indicative of their benign nature. p53 reactivity in concert with a lack of p21 up-regulation by immunohistochemistry suggests that a p53 mutation may be present in PN, although the immunohistochemical findings alone cannot exclude possible overexpression of wild-type p53. Regressive, involutional, or maturational changes were observed in sequential samples from 4 patients. No patient developed malignant melanoma or another melanocytic nevus-associated malignancy during the follow-up period. These findings underscore the similarities between PNs and the underlying CMN and suggest that maturational, proliferative, and apoptotic processes are involved in their clinical evolution.
The curated web: a recommendation challenge

In this paper we consider the application of content-based recommendation techniques to web curation services which allow users to curate and share topical collections of content (e.g. images, news, web pages etc.). Curation services like Pinterest are now a mainstay of the modern web and present a range of interesting recommendation challenges. In this paper we consider the task of recommending collections to users and evaluate a range of different content-based techniques across a variety of content signals. We present the results of a large-scale evaluation using data from the Scoop.it web page curation service
Biochemical marker as predictor of outcome in perinatal asphyxia.

Birth asphyxia is a leading cause of neonatal mortality in India. At present there is no reliable early marker to predict the outcome in these cases. We conducted this study to evaluate 8-hydroxy 2-deoxyguanosine (8-OHdG) as a biochemical marker for predicting outcome in perinatal asphyxia. Term neonates fulfilling the inclusion criteria were recruited in the study. Cord blood was collected immediately after birth. The concentration of 8-OHdG was analyzed using ELISA. These children were followed up till discharge from hospital with close monitoring for adverse events and morbidities. Neurodevelopmental assessment was done using Baroda developmental screening test up to the age of 6 months. The mean value of 8-OHdG was found to increase with severity of encephalopathy. 8-OHdG values were significantly higher among the cases that expired compared to those who survived. Developmental delay occurred in 29.4% cases. The 8-OHdG levels were significantly higher among the cases who developed developmental delay than those with normal development. It is concluded that, 8-OHdG is a good early serum biochemical marker in predicting the outcome in perinatal asphyxia
Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data

Motivation: Targeted interventions using RNA interference in combination with the measurement of secondary effects with DNA microarrays can be used to computationally reverse engineer features of upstream non-transcriptional signaling cascades based on the nested structure of effects. Results: We extend previous work by Markowetz et al., who proposed a statistical framework to score different network hypotheses. Our extensions go in several directions: we show how prior assumptions on the network structure can be incorporated into the scoring scheme by defining appropriate prior distributions on the network structure as well as on hyperparameters. An approach called module networks is introduced to scale up the original approach, which is limited to around 5 genes, to infer large-scale networks of more than 30 genes. Instead of the data discretization step needed in the original framework, we propose the usage of a beta-uniform mixture distribution on the P-value profile, resulting from differential gene expression calculation, to quantify effects. Extensive simulations on artificial data and application of our module network approach to infer the signaling network between 13 genes in the ER-α pathway in human MCF-7 breast cancer cells show that our approach gives sensible results. Using a bootstrapping and a jackknife approach, this reconstruction is found to be statistically stable. Availability: The proposed method is available within the Bioconductor R-package nem. Contact: h.froehlich@dkfz-heidelberg.de
The tissue distribution of the B7-2 costimulator in mice: abundant expression on dendritic cells in situ and during maturation in vitro

B7-2 is a recently discovered, second ligand for the CTLA-4/CD28, T cell signaling system. Using the GL-1 rat monoclonal antibody (mAb), we monitored expression of B7-2 on mouse leukocytes with an emphasis on dendritic cells. By cytofluorography, little or no B7-2 was detected on most cell types isolated from spleen, thymus, peritoneal cavity, skin, marrow, and blood. However, expression of B7-2 could be upregulated in culture. In the case of epidermal and spleen dendritic cells, which become highly immunostimulatory for T cells during a short period of culture, the upregulation of B7-2 was dramatic and did not require added stimuli. Lipopolysaccharide did not upregulate B7-2 levels on dendritic cells, in contrast to macrophages and B cells. By indirect immunolabeling, the level of staining with GL-1 mAb exceeded that seen with rat mAbs to several other surface molecules including intercellular adhesion molecule 1, B7-1, CD44, and CD45, as well as new hamster mAbs to CD40, CD48, and B7-1/CD80. Of these accessory molecules, B7-2 was a major species that increased in culture, implying a key role for B7-2 in the functional maturation of dendritic cells. B7- 2 was the main (> 90%) CTLA-4 ligand on mouse dendritic cells. When we applied GL-1 to tissue sections of a dozen different organs, clear-cut staining with B7-2 antigen was found in many. B7-2 staining was noted on liver Kupffer cells, interstitial cells of heart and lung, and profiles in the submucosa of the esophagus. B7-2 staining was minimal in the kidney and in the nonlymphoid regions of the gut, and was not observed at all in the brain. In the tongue, only rare dendritic cells in the oral epithelium were B7-2+, but reactive cells were scattered about the interstitial spaces of the muscle. In all lymphoid tissues, Gl-1 strongly stained certain distinct regions that are occupied by dendritic cells and by macrophages. For dendritic cells, these include the thymic medulla, splenic periarterial sheaths, and lymph node deep cortex; for macrophages, the B7-2-rich regions included the splenic marginal zone and lymph node subcapsular cortex. Splenic B7-2+ cells were accessible to labeling with GL-1 mAb given intravenously. Dendritic cell stimulation of T cells (DNA synthesis) during the mixed leukocyte reaction was significantly (35-65%) blocked by GL-1. (ABSTRACT TRUNCATED AT 400 WORDS)
Prevalence and severity of urogenital symptoms in postmenopausal women receiving endocrine therapy for breast cancer.

BACKGROUND Data from randomized trials in postmenopausal women receiving endocrine therapy for breast cancer would suggest that the incidence of significant urogenital symptoms is around 40%. As there are inherent reporting biases associated with clinical trials, we sought to assess the prevalence, severity, and effect of urogenital side effects of endocrine therapy in the non-trial setting. PATIENTS AND METHODS A cross-sectional survey study was undertaken and questionnaires used to assess vulvovaginal and urinary tract symptoms in a group of postmenopausal women receiving endocrine therapy for breast cancer. RESULTS A total of 251 women were surveyed. Sixty-three percent (158) reported urogenital symptoms. Vaginal dryness was the most common vaginal symptom, occurring in 121 women (48%). This was rated as severe or very severe in 56 of 121 (46%). Thirty-one of 251 (12%) women experienced urinary symptoms. A total of 68 women (27%) had used some form of treatment for vaginal symptoms. Nine women (4%) had considered discontinuing treatment because of urogenital side effects. CONCLUSION Urogenital side effects are common and often severe in women receiving endocrine therapy for breast cancer. The prevalence in this study was 63%, which is higher than that reported in the clinical trial literature. Less than one third of patients had used some form of treatment for these symptoms. This highlights the need for increased recognition and management of the urogenital side effects of estrogen deprivation therapy and raises the concern of the risk of non-compliance with potentially curative adjuvant therapy.
Closed Curves of Global bifurcations in Chua's equation: a Mechanism for their Formation

In this work, the presence of closed bifurcation curves of homoclinic and heteroclinic connections has been detected in Chua’s equation. We have numerically found and qualitatively described the mechanism of the formation/destruction of such closed curves. We relate this phenomenon to a failure of transversality in a curve of T-points in a three-dimensional parameter space.
A Pilot Efficacy and Tolerability Trial of Memantine for Essential Tremor

Objective:We studied the potential efficacy and tolerance of memantine for essential tremor in an open-treatment trial. Methods:Participants with upper-limb tremor were titrated to no more than 40 mg/d memantine, as monotherapy or as adjunct to stable antitremor medication, followed by a 12-week extension phase. Tremor was assessed in study 1 with accelerometry and in study 2 by blinded ratings of videotaped Washington Heights Inwood Genetic Essential Tremor (WHIGET) rating scale items. Subjects also rated their tremor treatment response and tremor-associated impairment on the Functional Disabilities scale. Results:In study 1, average accelerometry-measured tremor at last titration visit (average dose, 30.3 mg/d) did not change from baseline, but 2 of 9 subjects, taking 40 mg/d, had greater than 70% accelerometry tremor reduction. In study 2, 13 of 16 provided evaluable data. Average blinded rater-evaluated WHIGET scores were significantly different from baseline scores among those taking 20 mg/d (−12.7%; P < 0.05), but not at last titration visit (−8.4%; average dose, 30.4 mg/d), 40 mg/d (−14.1%), or at end-of-extension visit (−18.2%). Raters judged WHIGET scores as greater than 30% improved in 2 subjects. Unblinded subjects rated Functional Disabilities significantly improved at 30 to 40 but not at 10 to 20 mg/d, and tremor treatment response was positive at all doses. Adverse events were more common at higher doses and included dizziness, somnolence, and poor energy. Conclusions:These pilot results with small samples indicate that the average effect of memantine on tremor is mild or not significant. However, in a small subset of patients, memantine may confer meaningful tremor benefit.
Phase relationships between Antarctic and Greenland climate records

Abstract Comparison of climate records from Antarctic and Greenland ice cores shows that the two regions respond asynchronously during millennial-scale climate changes. the apparent out-of-phase relationship between the records has been described as a climate ``seesaw’’ in which cooling in the Northern Hemisphere is balanced by warming in the Southern Hemisphere. the same relationship has also been attributed to the initiation of climate-change events in the Southern Hemisphere, rather than the North Atlantic as is conventionally assumed. A simple statistical approach−band-pass filtering combined with lag–correlation tests−used to examine the phase relationships in more detail shows that neither an anti-phase nor a phase-lag relationship adequately describes the observations. Whereas Antarctic and Greenland climate records do exhibit approximate anti-phase behavior about 50% of the time, they are generally in phase during cooling. A phase lead of Southern Hemisphere climate of 1000–1600 years is statistically indistinguishable from a lag of 400–800 years, whether for Dansgaard–Oeschger, Heinrich or longer-duration events. the ``seesaw’’ or ``Southern lead’’ appearance of the data arises from the fundamentally different characteristics of the climate time series, most importantly the absence of rapid warming events in Antarctica comparable to those in Greenland. to be consistent with the observations, climate models will need to capture these characteristics, in addition to reproducing the correct phase relationships.
Evaluation of the Snow Simulations from the Community Land Model, Version 4 (CLM4)

AbstractThis paper evaluates the simulation of snow by the Community Land Model, version 4 (CLM4), the land model component of the Community Earth System Model, version 1.0. 4 (CESM1.0.4). CLM4 was run in an offline mode forced with the corrected land-only replay of the Modern-Era Retrospective Analysis for Research and Applications (MERRA-Land) and the output was evaluated for the period from January 2001 to January 2011 over the Northern Hemisphere poleward of 30°N. Simulated snow-cover fraction (SCF), snow depth, and snow water equivalent (SWE) were compared against a set of observations including the Moderate Resolution Imaging Spectroradiometer (MODIS) SCF, the Interactive Multisensor Snow and Ice Mapping System (IMS) snow cover, the Canadian Meteorological Centre (CMC) daily snow analysis products, snow depth from the National Weather Service Cooperative Observer (COOP) program, and Snowpack Telemetry (SNOTEL) SWE observations. CLM4 SCF was converted into snow-cover extent (SCE) to compare with MODIS.
Rapid Homeostatic Plasticity of Intrinsic Excitability in a Central Pattern Generator Network Stabilizes Functional Neural Network Output

Neurons and networks undergo a process of homeostatic plasticity that stabilizes output by integrating activity levels with network and cellular properties to counter longer-term perturbations. Here we describe a rapid compensatory interaction among a pair of potassium currents, IA and IKCa, that stabilizes both intrinsic excitability and network function in the cardiac ganglion of the crab, Cancer borealis. We determined that mRNA levels in single identified neurons for the channels which encode IA and IKCa are positively correlated, yet the ionic currents themselves are negatively correlated, across a population of motor neurons. We then determined that these currents are functionally coupled; decreasing levels of either current within a neuron causes a rapid increase in the other. This functional interdependence results in homeostatic stabilization of both the individual neuronal and the network output. Furthermore, these compensatory increases are mechanistically independent, suggesting robustness in the maintenance of neural network output that is critical for survival. Together, we generate a complete model for homeostatic plasticity from mRNA to network output where rapid post-translational compensatory mechanisms acting on a reservoir of channels proteins regulated at the level of gene expression provide homeostatic stabilization of both cellular and network activity.
LOCATING SOIL BOUNDARIES USING MAGNETIC SUSCEPTIBILITY

Topsoil (0 to 15 cm) samples which included three soil series and three drainage classes were taken at 1 m intervals along a 200 m transect through native prairie in southern Oklahoma. Magnetic susceptibility was measured on every sample, particle size distribution and organic matter content on alternate samples, and elevations at 5 m intervals along the transect. Magnetic susceptibility values were larger on the summit and sideslopes, smallest in the drainageway, and related to sand content (parent material) and soil wetness (landscape position). The sand content of the soil followed a similar pattern to the magnetic susceptibility. Clay and organic matter content increased slightly along the transect and did not appear to be related to landscape position or soils. Semivario-grams based on magnetic susceptibility, sand, and silt contents displayed ranges of 59 to 64 m, indicating boundaries at approximately 60 and 120 m; these roughly separated the well- and moderately well-drained soils from the poorly-drained soil. A moving split window technique was used as a numerical method for boundary location. Textural components provided a general indication of the boundaries among the three soil series, but magnetic susceptibility data partitioned the transect with more distinct boundaries which clearly delineated the soil series. Magnetic susceptibility can be measured in situ at numerous locations much more quickly than texture, and additionally it accounts for drainage conditions of the soil. Its use in soil survey looks very promising.
Incorporating Singular Ratings into Collaborative Filtering

Collaborative filtering (CF) is an effective technique addressing the information overload problem, where each user is represented as a set of rating scores on items. Given a target user, conventional CF algorithms measure similarity between two users by utilizing each pair of ratin g scores on common rated items but discarding scores rated by either of them. In this paper, we called the former as dual ratingswhile the latter assingular ratings . Our experiments show that only about 10% ratings are dual ones and can be used for similarity evaluation while the left 90% are singul ar ones and discarded. For making full use of the limited data resource, in this paper, we present SingCF, which attempts to incorporate singular ratings for accuracy improvement o f CF algorithms. In particular, we first estimate the unrated scores for singular ratings and transform them into dual ones. Then we perform a CF process to discover neighborhood users and make predictions for each user. Experiments in comparison with the state-of-the-art methods demonstra te the promise of our approach.