Miracle-dz/UniFAR-FTUs huggingface dataset:
JOY: protein sequence-structure representation and analysis

MOTIVATION JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed to display 3D structural information in a sequence alignment and to help understand the conservation of amino acids in their specific local environments. RESULTS : The JOY representation now constitutes an essential part of the two databases of protein structure alignments: HOMSTRAD (http://www-cryst.bioc.cam.ac.uk/homstrad ) and CAMPASS (http://www-cryst.bioc.cam.ac. uk/campass). It has also been successfully used for identifying distant evolutionary relationships. AVAILABILITY The program can be obtained via anonymous ftp from torsa.bioc. cam.ac. uk from the directory /pub/joy/. The address for the JOY server is http://www-cryst.bioc. cam.ac. uk/cgi-bin/joy.cgi. CONTACT kenji@cryst.bioc. cam.ac. uk
Seizures in Alzheimer disease: who, when, and how common?

BACKGROUND Transient symptoms in Alzheimer disease (AD) are frequent and include seizures, syncope, and episodes of inattention or confusion. The incidence of seizures in AD and predictors of which patients with AD might be more predisposed to them is based primarily on retrospective studies and is not well established. OBJECTIVE To determine the incidence and predictors of new-onset unprovoked seizures. DESIGN Prospective cohort study. SETTING Three academic centers. Patients Four hundred fifty-three patients with probable AD observed prospectively from mild disease stages since 1992. Main Outcome Measure Informant interviews every 6 months included questions about whether the patient had a seizure (convulsion, fainting, or "funny" spell) and whether diagnosis or treatment for epilepsy or seizure was made. Two epileptologists independently retrospectively reviewed all available medical records for 52 patients with positive responses to either of these questions, and using a specific checklist form, events were diagnosed as to whether they were unprovoked seizures (intrarater concordance, kappa = 0.67). Diagnosis of unprovoked seizures constituted the event in survival analyses. Potential predictors included sex, age, race/ethnicity, educational achievement, duration of illness, baseline cognition and function, depression, medical comorbidities, and time-dependent use of cholinesterase inhibitors and neuroleptic agents, apolipoprotein E genotype, and previous electroencephalographic findings. RESULTS Over the course of 3518 visit-assessments (per patient: mean, 7.8; maximum, 27), 7 patients (1.5%) developed seizures. Younger age was associated with higher risk (hazard ratio, 1.23; 95% confidence interval, 1.08-1.41; P = .003 for each additional year of age) of seizure incidence. No other predictor was significant. The overall incidence of seizures was low (418 per 100 000 person-years of observation) although significantly higher than expected for idiopathic unprovoked seizures in similar age ranges of the general population (hazard ratio, 8.06; 95% confidence interval, 3.23-16.61). CONCLUSIONS Unprovoked seizures are uncommon in AD, but they do occur more frequently than in the general population. Younger age is a risk factor for seizures in AD.
New definitions of 6 clinical signs of perceptual disorder in children with cerebral palsy: an observational study through reliability measures.

BACKGROUND Recently authors have begun to emphasize the non-motor aspects of Cerebral Palsy and their influence on motor control and recovery prognosis. Much has been written about single clinical signs (i.e., startle reaction) but so far no definitions of the six perceptual signs presented in this study have appeared in literature. AIM This study defines 6 signs (startle reaction, upper limbs in startle position, frequent eye blinking, posture freezing, averted eye gaze, grimacing) suggestive of perceptual disorders in children with cerebral palsy and measures agreement on sign recognition among independent observers and consistency of opinions over time. DESIGN Observational study with both cross-sectional and prospective components. SETTING Fifty-six videos presented to observers in random order. Videos were taken from 19 children with a bilateral form of cerebral palsy referred to the Children Rehabilitation Unit in Reggio Emilia. PARTICIPANTS Thirty-five rehabilitation professionals from all over Italy: 9 doctors and 26 physiotherapists. METHODS Measure of agreement among 35 independent observers was compiled from a sample of 56 videos. Interobserver reliability was determined using the K index of Fleiss and reliability intra-observer was calculated by the Spearman correlation index between ranks (rho - ρ). Percentage of agreement between observers and Gold Standard was used as criterion validity. RESULTS Interobserver reliability was moderate for startle reaction, upper limb in startle position, adverted eye gaze and eye-blinking and fair for posture freezing and grimacing. Intraobserver reliability remained consistent over time. Criterion validity revealed very high agreement between independent observer evaluation and gold standard. CONCLUSIONS Semiotics of perceptual disorders can be used as a specific and sensitive instrument in order to identify a new class of patients within existing heterogeneous clinical types of bilateral cerebral palsy forms and could help clinicians in identifying functional prognosis. CLINICAL REHABILITATION IMPACT To provide clinicians with a definition of 6 clinical signs found in children with cerebral palsy in routine rehabilitation settings. Future research should explore the link between these signs and motor prognosis (i.e., time to independent walking).
Actinomyces species: A Danish Survey on Human Infections and Microbiological Characteristics

This study compared phenotypic and genotypic identification of Actinomyces strains, tested susceptibility to antibiotics and evaluated their clinical importance. Thirty-four Actinomyces strains were examined; sixteen type strains, and 18 clinical strains from different hospitals in Denmark from the period 2003-2005. Partial 16S rDNA sequencing using a stretch of 526 bases was used for genotypic identification. Susceptibility testing was done by E-test. The antibiotics examined were: benzylpenicillin, piperacillin with tazobactam, ceftriaxone, meropenem, erythromycin, clindamycin, linezolid, moxifloxacin, tetracycline and tigecycline. Clinical parameters were obtained by reviewing patient records. There was poor agreement between the phenotypic and genotypic identification. Phenotypic tests were helpful in identifying strains closely related by DNA sequences. The strains were sensitive to the examined antibiotics except for moxifloxacin to which most strains were resistant, and a few strains were resistant to meropenem and tetracycline. The clinical strains were from many different types of infections and locations. None of the patients was described as having typical actinomycetic lesions, and an apparently good outcome was obtained with different treatment regimens.
Personalized Medicine for Nervous System Manifestations of von Hippel–Lindau Disease

von Hippel–Lindau disease (VHL) is a familial neoplasia syndrome associated with multisystem tumor development. Depending on tumor type and location, current treatments for VHL-associated tumors can include a combination of chemotherapy, radiation therapy, and/or surgery. Central nervous system (CNS) manifestations of VHL include craniospinal hemangioblastomas and endolymphatic sac tumors (ELSTs). While the first-line treatment for both types of VHL-associated CNS tumors is surgery, the indications for treatment are patient specific and different for each tumor type. Although early sign/symptom formation is the primary indication for resection of craniospinal hemangioblastomas, radiographic discovery (asymptomatic and symptomatic) of ELSTs can be an indication for resection of ELSTs in VHL patients. Recently, research has revealed that specific VHL germline mutations may permit targeted medical treatments of not only CNS manifestations of VHL-associated tumors but also visceral tumors. Specifically, missense mutations can result in the translation of functional VHL protein (pVHL) that is rapidly degraded resulting in functional loss of the pVHL, and inhibitors of pVHL degradation may slow protein degradation and restore pVHL function. Emerging research will investigate the safety and practicality of using potential targeted therapies.
Full Security: Fuzzy Identity Based Encryption

At EUROCRYPT 2005, Sahai and Waters presented the Fuzzy Identity Based Encryption (Fuzzy-IBE) which could be used for biometrics and attribute-based encryption in the selective-identity model. When a secure Fuzzy-IBE scheme in the selective-identity model is transformed to full identity model it exist an exponential loss of security. In this paper, we use the CPA secure Gentry's IBE (exponent inversion IBE) to construct the first Fuzzy IBE that is fully secure without random oracles. In addition, the same technique is used to the modification of CCA secure Gentry's IBE which introduced by Kiltz and Vahlis to get the CCA secure Fuzzy IBE in the full-identity model.
Wheat Dehydrin DHN-5 Exerts a Heat-Protective Effect on β-Glucosidase and Glucose Oxidase Activities

Group-2 late embryogenesis abundant (LEA) proteins, also known as dehydrins, are claimed to stabilize macromolecules against damage caused by freezing, dehydration, ionic or osmotic stresses. However, their precise function remains unknown. Here, we investigated the effect of wheat dehydrin (DHN-5) protein on the activity and thermostability of two distinct enzymes, β-glucosidase (bglG) and glucose oxidase/peroxidase (GOD/POD) in vitro. The purified DHN-5 protein had the capacity to preserve and stabilize the activity of bglG subjected to heat treatment. In addition, DHN-5 stabilized oxidizing enzymes, as it improved reliability in measuring glucose concentrations with a glucose oxidase/peroxidase (GOD/POD) kit while the temperature increased from 37 to 70 °C. All together the data presented provide evidence that DHN-5 is a dehydrin able to preserve enzyme activities in vitro from adverse effects induced by heating.
Eccentric peak torque of the plantar and dorsiflexors is maintained in older women.

Although a relative preservation of eccentric (ECC) strength with age has been reported previously, this phenomenon has not been studied in lower leg muscles. Concentric (CONC) and ECC plantar (PF) and dorsiflexion (DF) in healthy active older women (OW; n = 16, age = 67 +/- 4 years) and younger women (YW; n = 16, age = 27 +/- 4 years) were studied. Passive resistive torque of the plantar flexors and average rate of torque development (RTD) for both DF and PF were also measured. The OW had CONC peak torques that were 74% and 89% of the YW for PF and DF, whereas ECC peak torques were 97% and 100% of the YW. ECC torque patterns were almost identical for both groups, but there were significant differences for passive resistive torque (OW > YW; p < .01) and CONC RTD (OW < YW; p < .05). While increased passive resistive torque did not prove to be influential in maintaining ECC strength with age, it had a negative effect on CONC DF function.
Partner Choice and the Marital College Premium

Several theoretical contributions have argued that the returns to schooling within marriage play a crucial role for human capital investments. Our paper empirical investigates the evolution of these returns over the last decades. We consider a frictionless matching framework a la Becker-Shapley-Shubik, in which the gain generated by a match between two individuals is the sum of as ystematic effect that only depends on the spouses’ education classes and a match-specific term that we treat as random; following Choo and Siow (2006), we assume the latter component has an additively separable structure. We derive a complete, theoretical characterization of the model. We show that if the supermodularity of the surplus function is invariant over time and errors have extreme value distributions, the model is overidentified even if the surplus function varies over time. We apply our method to US data on individuals born between 1943 and 1972. Our model fits the data very closely; moreover, we find that the deterministic part of the surplus is indeed supermodular and that, in line with theoretical predictions, the “marital college premium” has increased more for women than for men over the period.
Routing with multi-level social groups in Mobile Opportunistic Networks

Mobile Opportunistic Networks (MONs) are intermittently connected networks, such as pocket switched networks formed by human-carried mobile devices. Routing in MONs is very challenging as it must handle network partitioning, long delays, and dynamic topology. Flooding is a possible solution but with high costs. Most existing routing methods for MONs avoid the costly flooding by selecting one or multiple relays to deliver data during each encounter. How to pick the “good” relay from all encounters is a non-trivial task. To achieve efficient delivery of messages at low costs, in this paper, we propose a new group-based routing protocol in which the relay node is selected based on social group information obtained from historical encounters. We apply a simple formation method to build multi-level social groups, which summarizes the wide range of social relationships among all mobile participants. Our simulations demonstrate the efficiency and effectiveness of the proposed method by comparing it with several existing MON routing schemes.
Support driven reweighted ℓ1 minimization

In this paper, we propose a support driven reweighted ℓ1 minimization algorithm (SDRL1) that solves a sequence of weighted ℓ1 problems and relies on the support estimate accuracy. Our SDRL1 algorithm is related to the IRL1 algorithm proposed by Candès, Wakin, and Boyd. We demonstrate that it is sufficient to find support estimates with good accuracy and apply constant weights instead of using the inverse coefficient magnitudes to achieve gains similar to those of IRL1. We then prove that given a support estimate with sufficient accuracy, if the signal decays according to a specific rate, the solution to the weighted ℓ1 minimization problem results in a support estimate with higher accuracy than the initial estimate. We also show that under certain conditions, it is possible to achieve higher estimate accuracy when the intersection of support estimates is considered. We demonstrate the performance of SDRL1 through numerical simulations and compare it with that of IRL1 and standard ℓ1 minimization.
Differential response of equatorial Pacific phytoplankton to iron fertilization

Recent unenclosed iron‐fertilization experiments in the equatorial Pacific Ocean have shown that phytoplankton biomass can be increased substantially by the addition of iron. Analyses of size‐fractionated chlorophyll indicate that much of the increase during the most recent fertilization experiment, IronEx II, occurred in the >10‐um size fraction. We used flow cytometry, combined with taxon‐specific pigment measurements by high‐performance liquid chromatography (HPLC), to analyze the responses of five different groups of phytoplankton: Prochlorococcus, Synechococcus, ultraplankton, nanoplankton, and pennate diatoms. These results are unique in the suite of measurements from the IronEx studies in that they simultaneously examine individual cell properties, which are grazer independent, and population dynamics, which reflect the net result of growth and grazing. Our results show that the overall increase of chlorophyll a (Chl a) in the patch was due in part to increases in chlorophyll content per cell and in part to increases in cell numbers of specific groups. Cellular fluorescence was stimulated by iron addition in all five groups to a qualitatively similar degree and was correlated with taxon specific changes in cellular pigments. In terms of net cell growth, however, these groups responded very differently. The groups that dominated the community before the addition of iron increased at most twofold in cell number; Prochlorococcus actually decreased. In contrast, the initially rare pennate diatoms increased 15‐fold in number by the peak of the iron‐induced bloom. Within 1 week, this differential response led to a dramatic change in the phytoplankton community structure, from one dominated by picoplankton to one dominated by large diatoms. It is not known whether this shift would be sustained over extended periods of fertilization, a response that would ultimately change the structure of the food web.
Riemannian Geometry Applied to Detection of Respiratory States From EEG Signals: The Basis for a Brain–Ventilator Interface

Goal: During mechanical ventilation, patient-ventilator disharmony is frequently observed and may result in increased breathing effort, compromising the patient's comfort and recovery. This circumstance requires clinical intervention and becomes challenging when verbal communication is difficult. In this study, we propose a brain–computer interface (BCI) to automatically and noninvasively detect patient-ventilator disharmony from electroencephalographic (EEG) signals: a brain–ventilator interface (BVI). Methods: Our framework exploits the cortical activation provoked by the inspiratory compensation when the subject and the ventilator are desynchronized. Use of a one-class approach and Riemannian geometry of EEG covariance matrices allows effective classification of respiratory states. The BVI is validated on nine healthy subjects that performed different respiratory tasks that mimic a patient-ventilator disharmony. Results: Classification performances, in terms of areas under receiver operating characteristic curves, are significantly improved using EEG signals compared to detection based on air flow. Reduction in the number of electrodes that can achieve discrimination can be often desirable (e.g., for portable BCI systems). By using an iterative channel selection technique, the common highest order ranking, we find that a reduced set of electrodes ($n=6$ ) can slightly improve for an intrasubject configuration, and it still provides fairly good performances for a general intersubject setting. Conclusion: Results support the discriminant capacity of our approach to identify anomalous respiratory states, by learning from a training set containing only normal respiratory epochs. Significance: The proposed framework opens the door to BVIs for monitoring patient's breathing comfort and adapting ventilator parameters to patient respiratory needs.
Determinants of Male Partner Involvement in Promoting Deliveries by Skilled Attendants in Busia, Kenya

A cross-sectional study covering 380 male partners and their spouses was conducted in Busia district in Western Kenya to establish demographic, socio-economic and cultural factors that affect male partner participation in promoting deliveries by skilled attendants. The study showed a significant relationship between level of education (P=0.0000) and level of income (P=0.0004) of the male partner and his support for skilled delivery. Lack of knowledge by male partners of complications associated with delivery, cultural beliefs, high fees charged for deliveries at health facilities and “un-cooperative” health workers are major contributing factors to low male partner involvement in child birth activities. Improving the levels of education and income of male partners, addressing the cultural beliefs and practices, improving health care provider-client relationship and sensitizing men on complications associated with pregnancy and child birth can contribute significantly in enhancing male partner involvement in promoting deliveries by skilled attendants.
The EB virus genome in Daudi Burkitt's lymphoma cells has a deletion similar to that observed in a non‐transforming strain (P3HR‐1) of the virus.

Epstein‐Barr virus (EBV) DNA isolated from the frequently studied and unusual Burkitt's lymphoma cell line, Daudi, contains a 7.4‐kb deletion, similar to (but larger than) that found in a non‐transforming isolate of the virus, P3HR‐1. A comparison of EBV sequence in Daudi cells with that from a comparable region in a wild‐type, transforming strain of the virus (B95‐8) indicates that at least two of the previously identified RNAs, a highly repetitive sequence, and other interesting coding or structural features should be absent in Daudi EBV DNA as a consequence of the deletion. The information removed by the deletion, as well as that which might be generated by juxtaposition of two regions of the genome that are not adjacent in most strains of the virus are discussed.
Diagnostic Role of Conventional Ultrasonography and Shearwave Elastography in Asymptomatic Patients with Diffuse Thyroid Disease: Initial Experience with 57 Patients

Purpose Thyroid ultrasonography (US) is a useful diagnostic tool in the evaluation of diffuse thyroid disease (DTD), whereas shearwave elastography is a dynamic technique that can provide information about tissue hardness by using acoustic shearwaves remotely induced by a focused ultrasonic beam. This study aims at investigating the role of conventional US and shearwave elastography in the diagnosis of asymptomatic patients with DTD. Materials and Methods Fifty-seven patients who underwent both conventional US and shearwave elastography were included in this study. Interobserver variability of the three radiologists in assessment of underlying thyroid echogenicity on conventional US was analyzed. Diagnostic performances for diagnosing DTD on conventional US and shearwave elastography were calculated and compared. Results Fair agreement was observed in the identification of DTD with conventional US (kappa value=0.27). The area under the receiver operating characteristic curve (Az) were 0.52-0.585 on conventional US by three radiologists. The Az values when using the mean and maximum elasticity values as a diagnostic criteria for DTD were 0.619 and 0.59 on shearwave elastography. Patients with DTD showed higher mean [24.1±10 kilo-Pascals (kPa)] and maximum (36.4±13.3 kPa) elasticity values on shearwave elastography when compared to the normal group (23.4±10.8 kPa and 33.7±12.4 kPa, respectively), although without statistical significance (p=0.802 and p=0.452, respectively). Conclusion Conventional US did not show reliable interobserver agreement in the diagnosis of DTD. Although not statistically significant, shearwave elastography may provide additional information in the diagnosis of DTD. Therefore, larger prospective studies are needed to define the values of shearwave elastography for diagnosing DTD.