Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating the causal effect of zidovudine on CD4 count with a marginal structural model for repeated measures

Even in the absence of unmeasured confounding factors or model misspecification, standard methods for estimating the causal effect of a time‐varying treatment on the mean of a repeated measures outcome (for example, GEE regression) may be biased when there are time‐dependent variables that are simultaneously confounders of the effect of interest and are predicted by previous treatment. In contrast, the recently developed marginal structural models (MSMs) can provide consistent estimates of causal effects when unmeasured confounding and model misspecification are absent. We describe an MSM for repeated measures that parameterizes the marginal means of counterfactual outcomes corresponding to prespecified treatment regimes. The parameters of MSMs are estimated using a new class of estimators – inverse‐probability of treatment weighted estimators. We used an MSM to estimate the effect of zidovudine therapy on mean CD4 count among HIV‐infected men in the Multicenter AIDS Cohort Study. We estimated a potential expected increase of 5.4 (95 per cent confidence interval ‐1.8,12.7) CD4 lymphocytes/l per additional study visit while on zidovudine therapy. We also explain the theory and implementation of MSMs for repeated measures data and draw upon a simple example to illustrate the basic ideas. Copyright © 2002 John Wiley & Sons, Ltd.
Maximum expected accurate structural neighbors of an RNA secondary structure

Since RNA molecules regulate genes and control alternative splicing by allostery, that is, by switching between two distinct secondary structures, it is important to develop algorithms to predict RNA conformational switches. It has recently emerged that RNA secondary structure can be more accurately predicted by computing the maximum expected accurate (MEA) structure, rather than the minimum free energy (MFE) structure. The MEA structure S has maximum score equations unpaired qi, where first sum is taken over all base pairs (i, j) belonging to S, and the second sum is taken over all unpaired positions in S, and where pi,j [resp. qi] is the probability that i, j are paired [resp. i is unpaired] in the ensemble of low energy structures.
A Cultural Psychosocial Model for Depression in Elder Care Institutions: The Roles of Socially Supportive Activity and Self-Transcendence

This study (1) developed and tested the Socially Supportive Activity Inventory (SSAI) to assess the quantity and quality of socially supportive activities that institutionalized elders receive, and (2) tested the predicted relationships among the variables proposed in the hypothesized causal model, socially supportive activities, self-transcendence, and depression in institutionalized elders. For pilot testing psychometric properties of the SSAI, the content validity was 0.96. Test-retest reliability from a sample of 10 participants yielded stability coefficients of 0.76-1.00, indicating the SSAI is a highly relevant and reliable culturally-based instrument. In the main study, a total of 196 participants were recruited from eight elder care institutions. The results showed an elder’s expectation of filial responsibility did not have a moderating effect on the willingness to be/remain institutionalized and on perceived stress. An elder’s acceptance of institutionalization was significantly related to perceived stress and indirectly affected depression. The mediator effect of self-transcendence on the relationship between perceived stress and depression was supported. The participation of elderly residents in socially supportive activities demonstrated a moderating effect on the strength of a negative relationship between perceived stress and self-transcendence. In the modified model, an elder’s willingness to remain institutionalized, perceived stress, and self-transcendence were significant predictors of depression, accounting for 54.7% of variance. Self-transcendence was the best predictor of depression. These findings contribute to an awareness of importance of culture factors as potential stressors. These findings also help to explain how the psychosocial mechanism of participation in socially supportive activities and the perception of selftranscendence act on depressed elders.
Location-Based Mobile Relay Selection and Impact of Inaccurate Path Loss Model Parameters

In this paper we propose a relay selection scheme which uses collected location information together with a path loss model for relay selection, and analyze the performance impact of mobility and different error causes on this scheme. Performance is evaluated in terms of bit error rate by simulations. The SNR measurement based relay selection scheme proposed earlier is unsuitable for use with fast moving users in e.g. vehicular scenarios due to a large signaling overhead. The proposed location based scheme is shown to work well with fast moving users due to a lower signaling overhead. The required location accuracy was found to be comparable to the accuracy of standard GPS. As the scheme was found to be highly sensitive to NLOS situations with unknown attenuation, knowledge of obstacle locations obtained either by sensing online or from a map of obstacles, was identified as a prerequisite in these situations. As the location-based scheme relies on a path loss model to estimate link qualities and select relays, the sensitivity with respect to inaccurate estimates of the unknown path loss model parameters is investigated. The parameter ranges that result in useful performance were found to be wide enough to allow them to be estimated in practical systems.
Stutter-Free Speech Following Response-Contingent Time-Out From Speaking in Young Children Who Stutter

Purpose: The purpose of this study was two-fold: 1) to determine if response-contingent time-out from speaking (RCTO) could effectively reduce stuttering frequency in young children, and 2) to determine if differences in participant awareness, emotional state, speech timing, and utterance length could be detected following RCTO. Background: RCTO is a fundamental component of operant treatments used for stuttering. RCTO requires the individual to pause from speaking immediately after a stuttering behavior has occurred. Well-controlled experimental investigations over the past 30 years have consistently demonstrated the robust and immediate effects of RCTO on stuttering (Prins & Hubbard, 1988), but few studies have examined the possible mechanism(s) responsible for these effects. At present, the processes mediating reductions in stuttering following RCTO are unknown. Factors such as cognitive processes, changes in affect, and modification of speech production systems have been implicated as underlying mechanisms, but findings have been inconsistent and inconclusive (Prins & Hubbard, 1988). Method: A time-series single-subject A1BA2 experiment was conducted on each of 5 children between the ages of 4 and 7 years while they engaged in several different linguistic tasks. Stuttering frequency was measured to determine the effectiveness of RCTO. Articulation rate and mean length of utterance were calculated from stutter-free speech samples obtained from all phases of the experiment (baseline, treatment, extinction). Reports were also obtained from the children after completion of the
Rapid Retargetting of a Flexible Pointing System with Structure Mounted Sensors and Actuators

In this paper, active control of flexible structures through utilization of structure mounted sensors and actuators is considered. Specifically, dynamic feedback design utilizing signals from the accelerometer mounted on the structure is discussed. Furthermore, utilization of piezoceramics for sensing and actuation to provide a higher level of control for vibration damping is investigated. The flexible pointing system considered here is the test-bed at the Army Research Development Engineering Center (ARDEC), which is a scaled-down representation of real-life targetting systems. This setup is also a nice benchmark problem for system identification and different control design philosophies. The approaches advocated here are based on Youla's parametrization of stabilizing controllers, Wiener-Hopf design and decentralized frequency shaping. Modelling aspects for the setup, taking all the structural intricacies into account, are discussed. The preliminary results indicate a significant improvement in performance through utilization of these control schemes.
Long-term outcome at age 7–10 years after extreme prematurity – a prospective, two centre cohort study of children born before 25 completed weeks of gestation (1999–2003)

Abstract Objective: We aimed to determine the long-term neurodevelopmental outcome in extremely preterm infants of 22–23 completed weeks’ gestation as compared to infants of 24 weeks with immediate postnatal life support born in two German tertiary perinatal centres between 1999 and 2003. Methods: Children were assessed for cognitive and neurological outcomes at the age of 7–10 years. The test battery included a neurological examination, the Wechsler Intelligence Scale for children (WISC-IV) and the Frostigs Developmental Test of Visual Perception (DTVP-2). Gross motor function was classified according to the GMFCS and functional activity was assessed with the Lincoln Oseretzky Motor Development Scale (LOS KF 18). Results: Outcome data were available for 79/105 children. 75.9% of the entire study cohort showed no or mild impairment. There was no difference seen between the two gestational age groups. Risk factors for moderate or severe impairment were an intracerebral haemorrhage >II° and/or periventricular leukomalacia or a retinopathy of prematurity >II°. Neither the gestational age (GA) nor the birth weight was associated with long-term outcome. Conclusions: Gestational age was not a predictor for long-term impairment of preterm infants born <25 completed weeks’ GA. Other prognostic factors should be taken into account for counselling in the grey zone of viability.
Preserving Text Content from Historical Handwritten Documents

We propose a holistic, dynamic method to preserve text content with zero tolerance while removing marginal noise for historical handwritten document images. The key idea is to identify and analyze the region between the sharp peak at the edge and page frame of the text content at each margin. Depending on the proximity of the sharp peak to the text, the text content is then extracted from the document image. This method automatically adapts thresholds for each single document image and is directly applicable to gray-scale images. The proposed method is evaluated on four diverse handwritten historical datasets: Queensland State Archive (QSA), Saint Gall, Parzival and the Prosecution Project. Experimental results show that the proposed method achieves higher accuracy compared with other methods tested on the Saint Gall and Parzival datasets, whilst for the other two Australian datasets, which have been introduced here for the first time, the results are very encouraging.
High Resolution Genome-Wide Analysis of Chromosomal Alterations in Burkitt's Lymphoma

Additional chromosomal abnormalities are currently detected in Burkitt's lymphoma. They play major roles in the progression of BL and in prognosis. The genes involved remain elusive. A whole-genome oligonucleotide array CGH analysis correlated with karyotype and FISH was performed in a set of 27 Burkitt's lymphoma-derived cell lines and primary tumors. More than half of the 145 CNAs<2 Mb were mapped to Mendelian CNVs, including GSTT1, glutathione s-transferase and BIRC6, an anti-apoptotic protein, possibly predisposing to some cancers. Somatic cell line-specific CNVs localized to the IG locus were consistently observed with the 244 K aCGH platform. Among 136 CNAs >2 Mb, gains were found in 1q (12/27), 13q (7/27), 7q (6/27), 8q(4/27), 2p (3/27), 11q (2/27) and 15q (2/27). Losses were found in 3p (5/27), 4p (4/27), 4q (4/27), 9p (4/27), 13q (4/27), 6p (3/27), 17p (3/27), 6q (2/27),11pterp13 (2/27) and 14q12q21.3 (2/27). Twenty one minimal critical regions (MCR), (range 0.04–71.36 Mb), were delineated in tumors and cell lines. Three MCRs were localized to 1q. The proximal one was mapped to 1q21.1q25. 2 with a 6.3 Mb amplicon (1q21.1q21.3) harboring BCA2 and PIAS3. In the other 2 MCRs, 1q32.1 and 1q44, MDM4 and AKT3 appeared as possible drivers of these gains respectively. The 13q31.3q32. 1 <89.58–96.81> MCR contained an amplicon and ABCC4 might be the driver of this amplicon. The 40 Kb 2p16.1 <60.96–61> MCR was the smallest gained MCR and specifically encompassed the REL oncogene which is already implicated in B cell lymphomas. The most frequently deleted MCR was 3p14.1 <60.43–60.53> that removed the fifth exon of FHIT. Further investigations which combined gene expression and functional studies are essential to understand the lymphomagenesis mechanism and for the development of more effective, targeted therapeutic strategies.
Modulo scheduling for a fully-distributed clustered VLIW architecture

Clustering is an approach that many microprocessors are adopting in recent times in order to mitigate the increasing penalties of wire delays. We propose a novel clustered VLIW architecture which has all its resources partitioned among clusters, including the cache memory. A modulo scheduling scheme for this architecture is also proposed. This algorithm takes into account both register and memory inter-cluster communications so that the final schedule results in a cluster assignment that favors cluster locality in cache references and register accesses. It has been evaluated for both 2- and 4-cluster configurations and for differing numbers and latencies of inter-cluster buses. The proposed algorithm produces schedules with very low communication requirements and outperforms previous cluster-oriented schedulers.
Sub-terahertz amplification in a semiconductor superlattice with moving charge domains

We theoretically study the high-frequency response of charge domains traveling through a strongly coupled semiconductor superlattice with an applied harmonic electromagnetic signal. Our calculations show that the superlattice alone can amplify signals with a frequency close to the domain transient frequency. Moreover, we show that if the superlattice is connected to a resonator, amplification becomes possible for much higher frequencies of the external signal (several hundred GHz). These promising results open the way to using semiconductor superlattices as efficient sub-THz amplifiers.
Achievable sum-rates in Gaussian multiple-access channels with MIMO-AF-relay and direct links

We consider a single-antenna Gaussian multiple-access channel (MAC) with a multiple-antenna amplify-and-forward (AF) relay, where, contrary to many previous works, also the direct links between transmitters and receiver are taken into account. For this channel, we investigate two transmit schemes: Sending and relaying all signals jointly or using a time-division multiple-access (TDMA) structure, where only one transmitter uses the channel at a time. While the optimal relaying matrices and time slot durations are found for the latter scheme, we provide upper and lower bounds on the achievable sum-rate for the former one. These bounds are evaluated by Monte Carlo simulations, where it turns out that they are very close to each other. Moreover, these bounds are compared to the sum-rates achieved by the TDMA scheme. For the asymptotic case of high available transmit power at the relay, an analytic expression is given, which allows to determine the superior scheme.
Mitochondrial diversity and the origins of African and European cattle.

The nature of domestic cattle origins in Africa are unclear as archaeological data are relatively sparse. The earliest domesticates were humpless, or Bos taurus, in morphology and may have shared a common origin with the ancestors of European cattle in the Near East. Alternatively, local strains of the wild ox, the aurochs, may have been adopted by peoples in either continent either before or after cultural influence from the Levant. This study examines mitochondrial DNA displacement loop sequence variation in 90 extant bovines drawn from Africa, Europe, and India. Phylogeny estimation and analysis of molecular variance verify that sequences cluster significantly into continental groups. The Indian Bos indicus samples are most markedly distinct from the others, which is indicative of a B. taurus nature for both European and African ancestors. When a calibration of sequence divergence is performed using comparisons with bison sequences and an estimate of 1 Myr since the Bison/Bos Leptobos common ancestor, estimates of 117-275,000 B.P. and 22-26,000 B.P. are obtained for the separation between Indians and others and between African and European ancestors, respectively. As cattle domestication is thought to have occurred approximately 10,000 B.P., these estimates suggest the domestication of genetically discrete aurochsen strains as the origins of each continental population. Additionally, patterns of variation that are indicative of population expansions (probably associated with the domestication process) are discernible in Africa and Europe. Notably, the genetic signatures of these expansions are clearly younger than the corresponding signature of African/European divergence.
Should we be using statistics to define disease?

“Don’t worry about the physiology test—if everybody fails, everybody passes”, Anonymous, Jefferson Medical College, Fall 1977. The first few months of medical school caused anxiety in most students, who typically went from environments where they were well above the “norm” in their classes to one in which they were just average. At the same time, the volume and difficulty of the material one was expected to master increased dramatically, compared with undergraduate studies. The one hope students could hold onto was that tests were graded “on the curve” and as long as you did better than the bottom 5% of the class (the lower limit of normal (LLN)) you would pass. This is the origin of the phrase “if everyone fails, everyone passes”. At the time, unbeknownst to the students, there was a push in our medical school to move towards a more standardised minimal passing grade of, somewhat ironic to this discussion, 70%, that would allow better comparison between classes and schools. The argument here was that if, in fact, everyone failed (ie, scored less than the minimum passing grade), even if that was “normal”, it was not good. The conflict between what is statistically “normal” and statistically “abnormal”, and how these are defined, is central to a current controversy in the world of respiratory medicine. On one side of this debate is the idea that “normal” people lose lung function as they age, and because of the “normal” loss of elastic tissue in the lung, the forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) will also decrease with aging. Defenders of this position state that the definition of “abnormal” needs to …
The Role of Maternal Invalidation in the Development of BPD symptoms in Adolescent Girls

Specific parenting mechanisms contributing to feelings of emotional invalidation in children and adolescents have not been adequately explored in the development of borderline personality disorder (BPD). The work in this area has been limited by cross-sectional studies using retrospective reports of adult samples and a limited range of parenting measures, which may be subject to bias. This study extends previous work by exploring associations between maternal invalidation and adolescent symptoms of BPD, with a short-term longitudinal design involving three assessments across one year, at baseline (Time 1), 6 months (Time 2), and 12 months (Time 3). Observational data were collected on 74 mother-adolescent dyads during a structured conflict discussion task at Time 2. It was hypothesized that invalidating maternal responses during the structured conflict discussion, at Time 2, would be associated with BPD symptoms at Time 3, even after controlling for BPD symptoms at Time 1. Results indicated that critical maternal behaviors during the structured conflict discussion task were predictive of BPD symptoms 6 months later, even after controlling for initial BPD symptoms, indicating that invalidating parenting may play a role in the maintenance and development of BPD among at-risk adolescents. Lower positive dyadic behavior also predicted BPD symptoms 6 months later at trend levels, suggesting that the mother-adolescent relationship may also contribute to the development of BPD. Future directions and clinical implications are discussed.
Long-term infusion of nesfatin-1 causes a sustained regulation of whole-body energy homeostasis of male Fischer 344 rats

Nesfatin-1, the N-terminal fragment of nucleobindin 2 (NUCB2), is an 82 amino-acid peptide that inhibits food intake and exerts weight-reducing effects. Nesfatin-1 has been proposed as a potential anti-obesity peptide. However, studies to date have mainly focused on the acute satiety effects of centrally administered nesfatin-1. The main objective of our studies was to characterize the long-term/chronic effects of peripheral administration of nesfatin-1 on whole-body energy balance and metabolic partitioning in male Fischer 344 rats. Short-term (1 day) subcutaneous infusion of nesfatin-1 (50 μg/kg body weight/day) using osmotic mini-pumps increased spontaneous physical activity and whole-body fat oxidation during the dark phase. This was accompanied by decreased food intake and basal metabolic rate compared to saline infused controls. On the seventh day of nesfatin-1 infusion, cumulative food intake, and total spontaneous physical activity during the dark phase were significantly reduced and elevated, respectively. Meanwhile, intraperitoneal injection of nesfatin-1 only caused a dark phase specific reduction in food intake and an increase in physical activity. NUCB2 mRNA expression in the brain and stomach, as well as serum NUCB2 concentrations were significantly reduced after 24 h fasting, while a post-prandial increase in serum NUCB2 was found in ad libitum fed rats. Collectively, our results indicate that chronic peripheral administration of nesfatin-1 at the dose tested, results in a sustained reduction in food intake and modulation of whole body energy homeostasis.
Age- and Gender-Related Changes in Ligament Components

The age- and gender-related changes in extracellular matrix components (elastin, elastin cross-links, fibrillin, collagen and glycoprotein) and mineral components (calcium, Ca; phosphorus, P) in human lumbar yellow ligaments were investigated using samples obtained from surgical specimens. The mineral (Ca and P) contents increased with ageing (r=0·703 and r=0·772, respectively), whereas the contents of matrix components tended to decrease with ageing (elastin r= −0·261, elastin cross-links r= −0·213, fibrillin r= −0·494; collagen r= −0·322 and glycoprotein r= −0·143). Comparison of the male and female groups revealed that the ligament elastin content and elastin cross-links decreased in the male group, whereas the ligament collagen content decreased in the female group significantly in an age-dependent manner (r= −0·788, r= −0·753 and r= −0·721, respectively). These findings demonstrate age- and gender-related changes in mineral and matrix components (especially elastin and collagen) in the lumbar yellow ligaments in the Japanese population. It is suggested that elastin and collagen metabolism in ligaments changes both with age and according to gender.