LLukas22/scidocs huggingface dataset:
27.6 A 4GS/s 13b pipelined ADC with capacitor and amplifier sharing in 16nm CMOS

In recent years, we have seen the emergence of multi-GS/s medium-to-high-resolution ADCs. Presently, SAR ADCs dominate low-speed applications and time-interleaved SARs are becoming increasingly popular for high-speed ADCs [1,2]. However the SAR architecture faces two key problems in simultaneously achieving multi-GS/s sample rates and high resolution: (1) the fundamental trade-off of comparator noise and speed is limiting the speed of single-channel SARs, and (2) highly time-interleaved ADCs introduce complex lane-to-lane mismatches that are difficult to calibrate with high accuracy. Therefore, pipelined [3] and pipelined-SAR [4] remain the most common architectural choices for high-speed high-resolution ADCs. In this work, a pipelined ADC achieves 4GS/s sample rate, using a 4-step capacitor and amplifier-sharing front-end MDAC architecture with 4-way sampling to reduce noise, distortion and power, while overcoming common issues for SHA-less ADCs.
Standing in an unstable shoe increases postural sway and muscle activity of selected smaller extrinsic foot muscles.

Inactivity or the under-utilization of lower limb muscles can lead to strength and functional deficits and potential injury. Traditional shoes with stability and support features can overprotect the foot and potentially contribute to the deterioration of the smaller extrinsic foot muscles. Healthy subjects (n=28) stood in an unstable MBT (Masai Barefoot Technology) shoe during their work day for a 6-week accommodation period. A two-way repeated measures ANOVA was used to determine (i) if unstable shoe wear increased electromyographic (EMG) activity of selected extrinsic foot muscles and increased postural sway compared to standing barefoot and in a stable control shoe and (ii) if postural sway and muscle activity across footwear conditions differed between a pre- and post-accommodation testing visit. Using an EMG circumferential linear array, it was shown that standing in the unstable shoe increased activity of the flexor digitorum longus, peroneal (PR) and anterior compartment (AC) muscles of the lower leg. No activity differences for the larger soleus (SOL) were identified between the stable and unstable shoe conditions. Postural sway was greater while standing in the unstable shoe compared to barefoot and the stable control shoe. These findings suggest that standing in the unstable MBT shoe effectively activates selected extrinsic foot muscles and could have implications for strengthening and conditioning these muscles. Postural sway while standing in the unstable MBT shoe also decreased over the 6-week accommodation period.
Maxillary gap at 11-13 weeks' gestation: marker of cleft lip and palate.

OBJECTIVE
To describe a new sign of cleft lip and palate (CLP), the maxillary gap, which is visible in the mid-sagittal plane of the fetal face used routinely for measurement of nuchal translucency thickness.


METHODS
This was a retrospective study of stored images of the mid-sagittal view of the fetal face at 11-13 weeks' gestation in 86 cases of CLP and 86 normal controls. The images were examined to determine if a maxillary gap was present, in which case its size was measured.


RESULTS
In 37 (43.0%) cases of CLP the defect was isolated and in 49 (57.0%) there were additional fetal defects. In the isolated CLP group, the diagnosis of facial cleft was made in the first trimester in nine (24.3%) cases and in the second trimester in 28 (75.7%). In the group with additional defects, the diagnosis of facial cleft was made in the first trimester in 46 (93.9%) cases and in the second trimester in three (6.1%). A maxillary gap was observed in 96% of cases of CLP with additional defects, in 65% of those with isolated CLP and in 7% of normal fetuses. There was a large gap (>1.5 mm) or complete absence of signals from the maxilla in the midline in 69% of cases of CLP with additional defects, in 35% of those with isolated CLP and in none of the normal controls.


CONCLUSIONS
The maxillary gap is a new simple marker of possible CLP, which could increase the detection rate of CLP, especially in isolated cases.
Clinical implications of energetic problems in cardiovascular disease

Cardiac energy metabolism can be altered in many forms of heart disease, including ischemic heart disease, cardiac hypertrophy, heart failure, and cardiac arrhythmias. Some of these energy metabolic changes are beneficial and help the heart adapt to the presence of the underlying cardiac pathology. However, some of the changes can also be maladaptive and actually contribute to the severity of cardiovascular disease. Because of the importance of energy metabolism in mediating cardiovascular disease, optimization of cardiac energetics has recently emerged as a novel approach to treat cardiovascular disease. This includes increasing the efficiency of oxygen utilization by the heart, which can be achieved by shifting cardiac metabolism to favor the use of carbohydrates rather than fatty acids as a metabolic fuel. This can be attained by reducing the circulating concentrations of fatty acids to which the heart is exposed, by inhibiting the uptake of fatty acids into the mitochondria, by directly inhibiting the enzymes of fatty acid oxidation, or by directly stimulating glucose metabolism. Clinical studies using these approaches have shown promise in treating various cardiovascular diseases, including ischemic heart disease, acute myocardial infarction, cardiac surgery, and heart failure. One agent that uses this approach is trimetazidine, which directly inhibits cardiac fatty acid oxidation and has been shown to be clinically effective in treating ischemic heart disease and heart failure. The paper will review those alterations in energy metabolism that occur in ischemic heart disease and heart failure, and the promising clinical approach of switching energy metabolism from fatty acid to glucose oxidation as a therapy in heart disease. Heart Metab. 2006;32:9–17.
Polyantigenic Interferon-γ Responses Are Associated with Protection from TB among HIV-Infected Adults with Childhood BCG Immunization

BACKGROUND
Surrogate immunologic markers for natural and vaccine-mediated protection against tuberculosis (TB) have not been identified.


METHODS
HIV-infected adults with childhood BCG immunization entering the placebo arm of the DarDar TB vaccine trial in Dar es Salaam, Tanzania, were assessed for interferon gamma (IFN-γ) responses to three mycobacterial antigen preparations--secreted Mycobacterium tuberculosis antigens 85 (Ag85), early secretory antigenic target 6 (ESAT-6) and polyantigenic whole cell lysate (WCL). We investigated the association between the number of detectable IFN-γ responses at baseline and the subsequent risk of HIV-associated TB.


RESULTS
During a median follow-up of 3.3 years, 92 (9.4%) of 979 placebo recipients developed TB. The incidence of TB was 14% in subjects with no detectable baseline IFN-γ responses vs. 8% in subjects with response to polyantigenic WCL (P = 0.028). Concomitant responses to secreted antigens were associated with further reduction in the incidence of HIV-associated TB. Overall the percentage of subjects with 0, 1, 2 and 3 baseline IFN-γ responses to mycobacterial preparations who developed HIV-associated TB was 14%, 8%, 7% and 4%, respectively (P = 0.004). In a multivariate Cox regression model, the hazard of developing HIV-associated TB was 46% lower with each increment in the number of detectable baseline IFN-γ responses (P<0.001).


CONCLUSIONS
Among HIV-infected adults who received BCG in childhood and live in a TB-endemic country, polyantigenic IFN-γ responses are associated with decreased risk of subsequent HIV-associated TB.


TRIAL REGISTRATION
ClinicalTrials.gov NCT0052195.
Some connectivity based cluster validity indices

Identification of the correct number of clusters and the appropriate partitioning technique are some important considerations in clustering where several cluster validity indices, primarily utilizing the Euclidean distance, have been used in the literature. In this paper a new measure of connectivity is incorporated in the definitions of seven cluster validity indices namely, DB-index, Dunn-index, Generalized Dunn-index, PS-index, I-index, XB-index and SV-index, thereby yielding seven new cluster validity indices which are able to automatically detect clusters of any shape, size or convexity as long as they are well-separated. Here connectivity is measured using a novel approach following the concept of relative neighborhood graph. It is empirically established that incorporation of the property of connectivity sigonnectivity elative neighborhood graph ingle linkage clustering technique -means clustering technique nificantly improves the capabilities of these indices in identifying the appropriate number of clusters. The well-known clustering techniques, single linkage clustering technique and K-means clustering technique are used as the underlying partitioning algorithms. Results on eight artificially generated and three real-life data sets show that connectivity based Dunn-index performs the best as compared to all the other six indices. Comparisons are made with the original versions of these seven cluster validity indices.
Proverb comprehension reconsidered—‘theory of mind’ and the pragmatic use of language in schizophrenia

BACKGROUND
For decades, impaired proverb comprehension has been regarded as typical of schizophrenic thought disorder. Testing patients' proverb understanding has widely been abandoned, however, due to poor reliability and validity of the assessment procedures. Since the underlying cognitive deficit of impaired proverb interpretation remained obscure, this study sought to determine the relation of proverb understanding with other cognitive domains, particularly 'theory of mind' or 'mindreading', in schizophrenia.


METHODS
31 patients diagnosed with schizophrenia were assessed using a novel German Proverb Test [Barth, A., Küfferle, B., 2001. Die Entwicklung eines Sprichworttests zur Erfassung konkretistischer Denkstörungen bei schizophrenen Patienten. Nervenarzt 72, 853-858.], a 'theory of mind' test battery, a variety of executive functioning tests and verbal intelligence. Psychopathology was measured using the PANSS [Kay, S.R., Opler, L.A., Lindenmayer, J.P., 1989. The Positive and Negative Syndrome Scale (PANSS): rationale and standardisation. Br. J. Psychiatry 158 (suppl. 7), 59-67.]. Patients' task performance was compared to a group of healthy control persons.


RESULTS
'Theory of mind', executive functioning and intelligence were strongly correlated with patients' ability to interpret proverbs correctly. In a regression analysis 'theory of mind' performance predicted, conservatively estimated, about 39% of the variance of proverb comprehension in the patient group.


CONCLUSIONS
The ability to interpret such metaphorical speech that is typical of many proverbs crucially depends on schizophrenic patients' ability to infer mental states. Future studies may further address differences between schizophrenia subtypes or the relation to specific symptom clusters.
Effects of an angiotensin II receptor blocker on the impaired function of endothelial progenitor cells in patients with essential hypertension.

BACKGROUND
Endothelial progenitor cells (EPCs) induce neovascularization and repair vascular damage. We have demonstrated that EPC function is impaired in hypertensive rats with increases in oxidative stress and that angiotensin II receptor blockers improved the impaired function of EPCs. In this study, we investigated basal EPC functions in normotensive control subjects and patients with essential hypertension and the effect of losartan on EPC function in hypertensive patients.


METHODS
Eighteen normotensive control subjects and 36 patients with essential hypertension who were undergoing treatment participated in the study. Hypertensive patients were randomly selected to receive 50mg of losartan or 4 mg of trichlormethiazide daily for 4 weeks. Peripheral blood mononuclear cells were isolated and cultured to assay EPC colony formation. Blood pressure, biological examination, and oxidative stress were evaluated in all subjects.


RESULTS
The number of EPC colonies was significantly lower in patients with essential hypertension than in normotensive control subjects. EPC colony number was significantly and inversely correlated with systolic and diastolic blood pressure in all subjects. EPC colony number was significantly increased by treatment with losartan in patients with essential hypertension but not affected by treatment with trichlormethiazide.


CONCLUSIONS
EPC function was inversely correlated with blood pressure and was impaired in essential hypertension. Losartan significantly improved the impaired EPC function in hypertensive patients. Impaired EPC function may determine the cardiovascular complications in essential hypertension. The improvement of EPC function with the administration of angiotensin II receptor blockers is considered to be one of the cardiovascular protective effects.
Peptidoglycan Crosslinking Relaxation Promotes Helicobacter pylori's Helical Shape and Stomach Colonization

The mechanisms by which bacterial cells generate helical cell shape and its functional role are poorly understood. Helical shape of the human pathogen Helicobacter pylori may facilitate penetration of the thick gastric mucus where it replicates. We identified four genes required for helical shape: three LytM peptidoglycan endopeptidase homologs (csd1-3) and a ccmA homolog. Surrounding the cytoplasmic membrane of most bacteria, the peptidoglycan (murein) sacculus is a meshwork of glycan strands joined by peptide crosslinks. Intact cells and isolated sacculi from mutants lacking any single csd gene or ccmA formed curved rods and showed increased peptidoglycan crosslinking. Quantitative morphological analyses of multiple-gene deletion mutants revealed each protein uniquely contributes to a shape-generating pathway. This pathway is required for robust colonization of the stomach in spite of normal directional motility. Our findings suggest that the coordinated action of multiple proteins relaxes peptidoglycan crosslinking, enabling helical cell curvature and twist.
The evolution of jealousy

If a single deontic reasoning system handles deontic social contracts and deontic precautions, then performance on both should be impaired by neural damage to that system. But if they are handled by two distinct neurocognitive systems, as predicted by SCT and HMT, then neural trauma could cause a dissociation. Buller’s hypothesis fails again: focal brain damage can selectively impair social contract reasoning while leaving precautionary reasoning intact [5]. This dissociation within the domain of deontic rules has recently been replicated using neuroimaging [6]. Interpretations of social contract rules track SCT’s domain-specialized inference procedures: in [8], we refuted Buller-style logic explanations of social contract results for perspective change, switched rules, and ‘wants’ problems – facts he fails to mention, let alone discuss. Buller’s systematic inattention to large bodies of findings that conflict with his assertions is not due to lack of space in TICS – the pretence that these findings do not exist pervades his book, and its treatment of many areas of evolutionary psychology. (For further analysis, see www. psych.ucsb.edu/research/cep/buller.htm)
CAPITO - a web server-based analysis and plotting tool for circular dichroism data

MOTIVATION
Circular dichroism (CD) spectroscopy is one of the most versatile tools to study protein folding and to validate the proper fold of purified proteins. Here, we aim to provide a readily accessible, user-friendly and platform-independent tool capable of analysing multiple CD datasets of virtually any format and returning results as high-quality graphical output to the user.


RESULTS
CAPITO (CD Anaylsis and Plotting Tool) is a novel web server-based tool for analysing and plotting CD data. It allows reliable estimation of secondary structure content utilizing different approaches. CAPITO accepts multiple CD datasets and, hence, is well suited for a wide application range such as the analysis of temperature or pH-dependent (un)folding and the comparison of mutants.


AVAILABILITY
http://capito.nmr.fli-leibniz.de.


CONTACT
cwiede@fli-leibniz.de or mago@fli-leibniz.de


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Learning And-Or Model to Represent Context and Occlusion for Car Detection and Viewpoint Estimation

This paper presents a method for learning an And-Or model to represent context and occlusion for car detection and viewpoint estimation. The learned And-Or model represents car-to-car context and occlusion configurations at three levels: (i) spatially-aligned cars, (ii) single car under different occlusion configurations, and (iii) a small number of parts. The And-Or model embeds a grammar for representing large structural and appearance variations in a reconfigurable hierarchy. The learning process consists of two stages in a weakly supervised way (i.e., only bounding boxes of single cars are annotated). First, the structure of the And-Or model is learned with three components: (a) mining multi-car contextual patterns based on layouts of annotated single car bounding boxes, (b) mining occlusion configurations between single cars, and (c) learning different combinations of part visibility based on CAD simulations. The And-Or model is organized in a directed and acyclic graph which can be inferred by Dynamic Programming. Second, the model parameters (for appearance, deformation and bias) are jointly trained using Weak-Label Structural SVM. In experiments, we test our model on four car detection datasets-the KITTI dataset [1] , the PASCAL VOC2007 car dataset [2] , and two self-collected car datasets, namely the Street-Parking car dataset and the Parking-Lot car dataset, and three datasets for car viewpoint estimation-the PASCAL VOC2006 car dataset [2] , the 3D car dataset [3] , and the PASCAL3D+ car dataset [4] . Compared with state-of-the-art variants of deformable part-based models and other methods, our model achieves significant improvement consistently on the four detection datasets, and comparable performance on car viewpoint estimation.
Likelihood Ratio Gradient Estimation for Stochastic Systems

Consider a computer system having a CPU that feeds jobs to two input/output (I/O) devices having different speeds. Let &thgr; be the fraction of jobs routed to the first I/O device, so that 1 - &thgr; is the fraction routed to the second. Suppose that α = α(&thgr;) is the steady-sate amount of time that a job spends in the system. Given that &thgr; is a decision variable, a designer might wish to minimize α(&thgr;) over &thgr;. Since α(·) is typically difficult to evaluate analytically, Monte Carlo optimization is an attractive methodology. By analogy with deterministic mathematical programming, efficient Monte Carlo gradient estimation is an important ingredient of simulation-based optimization algorithms. As a consequence, gradient estimation has recently attracted considerable attention in the simulation community. It is our goal, in this article, to describe one efficient method for estimating gradients in the Monte Carlo setting, namely the likelihood ratio method (also known as the efficient score method). This technique has been previously described (in less general settings than those developed in this article) in [6, 16, 18, 21]. An alternative gradient estimation procedure is infinitesimal perturbation analysis; see [11, 12] for an introduction. While it is typically more difficult to apply to a given application than the likelihood ratio technique of interest here, it often turns out to be statistically more accurate.
 In this article, we first describe two important problems which motivate our study of efficient gradient estimation algorithms. Next, we will present the likelihood ratio gradient estimator in a general setting in which the essential idea is most transparent. The section that follows then specializes the estimator to discrete-time stochastic processes. We derive likelihood-ratio-gradient estimators for both time-homogeneous and non-time homogeneous discrete-time Markov chains. Later, we discuss likelihood ratio gradient estimation in continuous time. As examples of our analysis, we present the gradient estimators for time-homogeneous continuous-time Markov chains; non-time homogeneous continuous-time Markov chains; semi-Markov processes; and generalized semi-Markov processes. (The analysis throughout these sections assumes the performance measure that defines α(&thgr;) corresponds to a terminating simulation.) Finally, we conclude the article with a brief discussion of the basic issues that arise in extending the likelihood ratio gradient estimator to steady-state performance measures.
DNA double-strand break repair

The integrity of genomic DNA is crucial for its function. And yet, DNA in living cells is inherently unstable. It is subject to mechanical stress and to many types of chemical modification that may lead to breaks in one or both strands of the double helix. Within the cell, reactive oxygen species generated by normal respiratory metabolism can cause double-strand breaks, as can stalled DNA replication. External agents that cause double-strand breaks include ionizing radiation and certain chemotherapeutic drugs. DNA double-strand breaks are also made and repaired during meiosis when recombination takes place between paired homologous chromosomes, during the rearrangement of immunoglobulin gene segments in lymphocyte development and during integration of certain mobile genetic elements and viruses into the host cell DNA. It is difficult to know how often double-strand breaks occur in the genome of a cell not exposed to external DNA-damaging agents, but we know from work with yeast cells that one persistent DNA double-strand break can be sufficient to trigger the death of a cell. If double-strand breaks go unrepaired in mammalian cells, they can also cause gene deletion, chromosome loss and other chromosomal aberrations that might ultimately produce cancers. DNA double-strand breaks are repaired by means of two main mechanisms: nonhomologous end joining and homologous recombination (see Figure 1). Both mechanisms operate in all eukaryotic cells that have been examined but the relative contribution of each mechanism varies. For example, most mammalian cells seem to favour nonhomologous end joining (also called ‘illegitimate recombination’), whereas homologous recombination is more common in the budding yeast Saccharomyces cerevisiae. One possible reason for this difference might be the prevalence in mammalian cells of repetitive sequences, which could lead to gene amplification or deletion if homologous recombination were common. In addition to these main mechanisms, DNA double-strand breaks can be repaired by means of single-strand annealing between adjacent repeated DNA sequences, which involves deletion of the intervening DNA (see Figure 1). This article focuses mainly on nonhomologous end joining, the best-characterized mammalian DNA double-strand break repair mechanism.