Miracle-dz/UniFAR-FTUs huggingface dataset:
Mucoid morphotype variation of Burkholderia multivorans during chronic cystic fibrosis lung infection is correlated with changes in metabolism, motility, biofilm formation and virulence.

Burkholderia cepacia complex (Bcc) bacteria are opportunistic pathogens infecting hosts such as cystic fibrosis (CF) patients. Long-term Bcc infection of CF patients' airways has been associated with emergence of phenotypic variation. Here we studied two Burkholderia multivorans clonal isolates displaying different morphotypes from a chronically infected CF patient to evaluate trait development during lung infection. Expression profiling of mucoid D2095 and non-mucoid D2214 isolates revealed decreased expression of genes encoding products related to virulence-associated traits and metabolism in D2214. Furthermore, D2214 showed no exopolysaccharide production, lower motility and chemotaxis, and more biofilm formation, particularly under microaerophilic conditions, than the clonal mucoid isolate D2095. When Galleria mellonella was used as acute infection model, D2214 at a cell number of approximately 7 × 10⁶ c.f. u. caused a higher survival rate than D2095, although 6 days post-infection most of the larvae were dead. Infection with the same number of cells by mucoid D2095 caused larval death by day 4. The decreased expression of genes involved in carbon and nitrogen metabolism may reflect lower metabolic needs of D2214 caused by lack of exopolysaccharide, but also by the attenuation of pathways not required for survival. As a result, D2214 showed higher survival than D2095 in minimal medium for 28 days under aerobic conditions. Overall, adaptation during Bcc chronic lung infections gave rise to genotypic and phenotypic variation among isolates, contributing to their fitness while maintaining their capacity for survival in this opportunistic human niche.
A low‐complexity turbo MUD for MU–MIMO SC‐FDMA systems

In order to provide high‐quality services, current communication systems require high data‐transmission rate and good error performance. Single carrier‐frequency division multiple access (SC‐FDMA) has been adopted as the uplink transmission standard in fourth generation cellular network to enable the power efficiency transmission in mobile station. Multi‐user multiple‐input multiple‐output (MU–MIMO) technologies are adopted in many standards to enhance the data rate and the link robustness. By combining MU–MIMO techniques with the SC‐FDMA modulation scheme, MU–MIMO SC‐FDMA systems can achieve high data rates over broadband wireless channels. For MU–MIMO SC‐FDMA systems, possible detection techniques include zero‐forcing detection, minimum mean squared error detection and maximum likelihood detection (MLD). Among these schemes, MLD is optimal, but its complexity grows exponentially with the number of symbols detected. As a result, there are demands for near MLD schemes that provide similar performance with less complexity. In this paper, we consider the MU–MIMO SC‐FDMA communication and propose a low‐complexity and high‐performance turbo receiver for the systems. Some simulation examples for uplink scenario are given to demonstrate the effectiveness of the proposed scheme. Copyright © 2015 John Wiley & Sons, Ltd.
ISAO: An Intelligent System of Opinions Analysis

Today, the need to automatically process opinions is strongly felt. It is in this context that we situate this work whose objective is to contribute to the achievement of opinions analysis system, enabling a binary classification on a set of textual data. For this, we studied and evaluated several methods, Support Vector Machines (SVM) and Naïve Bayes (NB), on a corpus composed of 500 journals films. These models have not been satisfactory. To improve the results we have introduced a pre-treatment phase or standardization corpus before classification; this phase has improved the quality of the classification.
The spectrum of behavioral responses to cholinesterase inhibitor therapy in Alzheimer disease.

BACKGROUND Behavioral abnormalities are common in Alzheimer disease (AD); cholinergic treatment reduces the behavioral disturbances of some patients with AD. Characterizing the pretreatment profile of patients who are likely to respond to cholinergic therapy will aid the efficient use of clinical resources. OBJECTIVE To determine the baseline behavioral profile for 86 patients with AD treated with the cholinesterase inhibitor donepezil hydrochloride. METHODS Open-label retrospective study of treatment-related behavioral assessments. Based on previous double-blind placebo-controlled experience using the Neuropsychiatric Inventory (NPI), patients were divided into responder (> or =4-point total NPI score decrease, indicating improvement), unchanged (+/-3-point total NPI score change), or nonresponder (> or =4-point total NPI score increase, indicating worsening) groups. The Mini-Mental State Examination assessed cognitive response. RESULTS Behavioral improvement was seen in 35 patients (41%), worsening in 24 (28%), and no change in 27 (31%). Comparison of profiles in behavioral responders vs nonresponders revealed significantly worse delusions (P = .04), agitation (P = .04), depression (P = .006), anxiety (P = .02), apathy (P = .003), disinhibition (P = .02), and irritability (P<.001) at baseline in responders. Five behaviors changed significantly from baseline, improving for the responders and worsening for the nonresponders: delusions (P = .003 for nonresponders, P = .004 for responders), agitation (P = .01), anxiety (P = .006 for nonresponders, P = .004 for responders), disinhibition (P = .02 for nonresponders, P = .05 for responders), and irritability (P = .003 for nonresponders, P = .001 for responders). The behavioral changes were dose dependent. Cognition did not change significantly with donepezil treatment within any group. CONCLUSIONS Donepezil has psychotropic properties, and pretreatment behaviors help predict patients' responses to treatment.
The constrained MUSIC problem

The MUSIC-based direction-of-arrival (DOA) method is generalized to include constraints involving known signal information. Projection operators are used to constrain the noise subspace to be orthogonal to a set of prespecified direction vectors. By incorporating known source directions, the estimation of unknown source directions can be significantly improved. Simulations are performed over a wide range of scenarios to demonstrate the usefulness of the approach. >
Neural Bases of Rapid Word Learning

Humans are unique in developing large lexicons as their communication tool; to achieve this, they are able to learn new words rapidly. However, neural bases of this rapid learning, which may be an expression of a more general cognitive mechanism likely rooted in plasticity at cellular and synaptic levels, are not yet understood. In this update, the author highlights a selection of recent studies that attempted to trace word learning in the human brain noninvasively. A number of brain areas, most notably in hippocampus and neocortex, appear to take part in word acquisition. Critically, the currently available data not only demonstrate the hippocampal role in rapid encoding followed by slow-rate consolidation of cortical word memory traces but also suggest immediate neocortical involvement in the word memory trace formation. Echoing early behavioral studies in ultra-rapid word learning, the reviewed neuroimaging experiments can be taken to suggest that our brain may effectively form new cortical circuits online, as it gets exposed to novel linguistic patterns in the sensory input.
A Cluster of Metabolic Defects Caused by Mutation in a Mitochondrial tRNA

Hypertension and dyslipidemia are risk factors for atherosclerosis and occur together more often than expected by chance. Although this clustering suggests shared causation, unifying factors remain unknown. We describe a large kindred with a syndrome including hypertension, hypercholesterolemia, and hypomagnesemia. Each phenotype is transmitted on the maternal lineage with a pattern indicating mitochondrial inheritance. Analysis of the mitochondrial genome of the maternal lineage identified a homoplasmic mutation substituting cytidine for uridine immediately 5′ to the mitochondrial transfer RNAIle anticodon. Uridine at this position is nearly invariate among transfer RNAs because of its role in stabilizing the anticodon loop. Given the known loss of mitochondrial function with aging, these findings may have implications for the common clustering of these metabolic disorders.
Critical Role for Mouse Hus1 in an S-Phase DNA Damage Cell Cycle Checkpoint

ABSTRACT Mouse Hus1 encodes an evolutionarily conserved DNA damage response protein. In this study we examined how targeted deletion of Hus1 affects cell cycle checkpoint responses to genotoxic stress. Unlike hus1− fission yeast (Schizosaccharomyces pombe) cells, which are defective for the G2/M DNA damage checkpoint, Hus1-null mouse cells did not inappropriately enter mitosis following genotoxin treatment. However, Hus1-deficient cells displayed a striking S-phase DNA damage checkpoint defect. Whereas wild-type cells transiently repressed DNA replication in response to benzo(a)pyrene dihydrodiol epoxide (BPDE), a genotoxin that causes bulky DNA adducts, Hus1-null cells maintained relatively high levels of DNA synthesis following treatment with this agent. However, when treated with DNA strand break-inducing agents such as ionizing radiation (IR), Hus1-deficient cells showed intact S-phase checkpoint responses. Conversely, checkpoint-mediated inhibition of DNA synthesis in response to BPDE did not require NBS1, a component of the IR-responsive S-phase checkpoint pathway. Taken together, these results demonstrate that Hus1 is required specifically for one of two separable mammalian checkpoint pathways that respond to distinct forms of genome damage during S phase.
Comorbidity of psychiatric diagnoses with posttraumatic stress disorder in survivors of childhood trauma.

OBJECTIVE This study examines posttraumatic stress disorder (PTSD) symptoms, trauma exposure, gender, and diagnostic comorbidity in a sample of 59 Cambodian young adults (29 male and 30 female) who survived massive trauma as children. METHOD Psychiatric diagnoses were made using the Structured Clinical Interview for DSM-III-R-Non-Patient version, a structured diagnostic interview, and trauma exposure was measured with a Traumatic Life Events Questionnaire. RESULTS A significant number of those with PTSD (59%) had one or more additional DSM-III-R Axis I disorders. Major depression and generalized anxiety disorder were the most common comorbid disorders. Somatoform pain disorder was also found to coexist with PTSD but only among females. Women were also found to have higher levels of both current and lifetime PTSD symptoms. CONCLUSION Trauma symptoms were related to exposure and exposure was related to age, but age was not related to symptoms. The findings suggest that the significant levels of comorbid diagnoses previously found to exist with PTSD in people traumatized as adults can be found among survivors of massive childhood trauma. Also, the rate of PTSD diagnoses found in this sample 15 years after the trauma of Pol Pot is comparable to findings previously reported in studies of Cambodian youths and shows that the effects of trauma experienced in childhood persist into early adulthood.
Changes in the alternative electron sinks and antioxidant defence in chloroplasts of the extreme halophyte Eutrema parvulum (Thellungiella parvula) under salinity.

BACKGROUND AND AIMS Eutrema parvulum (synonym, Thellungiella parvula) is an extreme halophyte that thrives in high salt concentrations (100-150 mm) and is closely related to Arabidopsis thaliana. The main aim of this study was to determine how E. parvulum uses reactive oxygen species (ROS) production, antioxidant systems and redox regulation of the electron transport system in chloroplasts to tolerate salinity. METHODS Plants of E. parvulum were grown for 30 d and then treated with either 50, 200 or 300 mm NaCl. Physiological parameters including growth and water relationships were measured. Activities of antioxidant enzymes were determined in whole leaves and chloroplasts. In addition, expressions of chloroplastic redox components such as ferrodoxin thioredoxin reductases (FTR), NADPH thioredoxin reductases (NTRC), thioredoxins (TRXs) and peroxiredoxins (PRXs), as well as genes encoding enzymes of the water-water cycle and proline biosynthesis were measured. KEY RESULTS Salt treatment affected water relationships negatively and the accumulation of proline was increased by salinity. E. parvulum was able to tolerate 300 mm NaCl over long periods, as evidenced by H2O2 content and lipid peroxidation. While Ca(2+) and K(+) concentrations were decreased by salinity, Na(+) and Cl(-) concentrations increased. Efficient induction of activities and expressions of water-water cycle enzymes might prevent accumulation of excess ROS in chloroplasts and therefore protect the photosynthetic machinery in E. parvulum. The redox homeostasis in chloroplasts might be achieved by efficient induction of expressions of redox regulatory enzymes such as FTR, NTRC, TRXs and PRXs under salinity. CONCLUSIONS E. parvulum was able to adapt to osmotic stress by an efficient osmotic adjustment mechanism involving proline and was able to regulate its ion homeostasis. In addition, efficient induction of water-water cycle enzymes and other redox regulatory components such as TRXs and PRXs in chloroplasts were able to protect the chloroplasts from salinity-induced oxidative stress.
Effects of Combined Estrogen and Progesterone on Brain Infarction in Reproductively Senescent Female Rats

Recent data from the Women's Health Initiative have highlighted many fundamental issues about the utility and safety of long-term estrogen use in women. Current hormone replacement therapy for postmenopausal women incorporates progestin with estrogen, but it is uncertain if combined therapy provides major cerebrovascular risks or benefits to these women. No experimental animal stroke studies have examined combined hormone administration. The authors tested the hypothesis that combined hormone treatment reduces ischemic injury in middle-aged female rat brain. Reproductively senescent female rats underwent 2-hour middle cerebral artery occlusion (MCAO) followed by 22 hours reperfusion. Estrogen implants were placed subcutaneously at least 7 days before MCAO, and progesterone intraperitoneal injections were given 30 minutes before MCAO, at initiation, and at 6 hours of reperfusion. Rats received no hormone, a 25-μg estrogen implant, a 25-μg estrogen implant plus 5 mg/kg intraperitoneal progesterone, or 5 mg/kg intraperitoneal progesterone. Cortical, caudoputamen, and total infarct volumes were assessed by 2,3,5-triphenyltetrazolium chloride staining and digital image analysis at 22 hours reperfusion. Cortical and total infarct volumes, except in the acute progesterone-treated group, were significantly attenuated in all estrogen-alone and combined hormone-treated groups. There were no significant differences in caudoputamen infarct volumes in all hormone-treated groups as compared with untreated rats. These data have potential clinical implications relative to stroke for postmenopausal women taking combined hormone replacement therapy.
Soft glass spiral photonic crystal fiber for large nonlinearity and high birefringence

This paper presents a soft glass spiral photonic crystal fiber with circular air holes for achieving high birefringence, large nonlinearity and large negative dispersion. The material used here for designing the fiber is soft glass (SF-57). A central defect air hole is being introduced in the core for achieving high birefringence and for different ellipticity ratios the effect of various optical properties of a photonic crystal fiber are studied. The structure proposed has a high birefringence in the order of 10 –2 , high nonlinearity of 5828 W –1 km –1 and high negative dispersion of –1546.6 ps/nm·km at 0.850 μm. A numerical approach based on the finite element method is used for the design and simulation of the structure. Due to the optimization in the cladding air holes, the fiber can be used as polarization maintaining fibers, in dispersion compensation and other nonlinear applications.
An Effective Approach for Obtaining Optimal Sampling Windows for Population Pharmacokinetic Experiments

This paper describes an effective approach for optimizing sampling windows for population pharmacokinetic experiments. Sampling windows has been proposed for population pharmacokinetic experiments that are conducted in late phase drug development programs where patients are enrolled in many centers and out-patient clinic settings. Collection of samples under this uncontrolled environment at fixed times may be problematic and can result in uninformative data. A sampling windows approach is more practicable, as it provides the opportunity to control when samples are collected by allowing some flexibility and yet provide satisfactory parameter estimation. This approach uses D -optimality to specify time intervals around fixed D -optimal time points that results in a specified level of efficiency. The sampling windows have different lengths and achieve two objectives: the joint sampling windows design attains a high specified efficiency level and also reflects the sensitivities of the plasma concentration-time profile to parameters. It is shown that optimal sampling windows obtained using this approach are very efficient for estimating population PK parameters and provide greater flexibility in terms of when samples are collected.
Four-Year Persistence of a Single Candida albicans Genotype Causing Bloodstream Infections in a Surgical Ward Proven by Multilocus Sequence Typing

ABSTRACT The present study represents the first application of multilocus sequence typing to retrospectively investigate a suspected outbreak of Candida albicans bloodstream infection cases that occurred in the same hospital ward between July 1987 and October 1991. Results demonstrated that eight bloodstream infections were caused by the same strain, endemic in the ward, over a 4-year period.
A new robustness optimization methodology for MEMS-IC systems

MEMS based sensor circuits are traditionally designed separately using CAD tools specific to each energy domain (mechanical and electrical). This paper presents a new approach for the robustness optimization of a MEMS-IC system. The new methodology is exemplified for a MEMS microphone with readout circuit. The design parameters of both the MEMS and the IC part are subject to optimization. Advanced methods for robustness analysis and optimization in consideration of operating and process parameters, developed for ICs, are transferred to MEMS based sensor circuits. The optimization succeeds only when considering both mechanical and electrical parameters. To save CPU time, a reduced-order model is used for the MEMS part. To integrate the generation of the simplified model into the optimization flow, a new simulation-in-a-loop flow based on commercial tools is implemented.
Characterization of mutations affecting the osmoregulated proU promoter of Escherichia coli and identification of 5' sequences required for high-level expression

Expression of the Escherichia coli proU operon, which encodes an efficient uptake system for the osmoprotectant glycine betaine, is strongly increased in cells grown at high osmolarity. We isolated 182 independent spontaneous mutants with elevated expression of the chromosomal phi(proV-lacZ) (Hyb2) fusion at low osmolarity. Genetic analysis demonstrated that eight of these mutant strains carried mutations closely linked to the fusion, whereas all others carried mutations that appeared to be in osmZ. All of the mutations resulted in increased but still osmoregulated expression of the phi(proV-lacZ)(Hyb2) fusion. The proU-linked mutants carried an identical point mutation (proU603) which changes the -35 sequence of the proU promoter from TTGCCT to TTGACT and thereby increases the homology of the -35 region to the consensus sequence (TTGACA) of E. coli promoters. We also selected for mutants with decreased expression of the plasmid pOS7-encoded phi(proV-lacZ)(Hyb2) fusion and isolated a plasmid with an IS1 insertion (proU607) between the proU -10 and -35 regions. This insertion creates a hybrid promoter and drastically reduces expression of the fusion but does not abolish its osmotic regulation. Deletion analysis of chromosomal sequences 5' to the proU promoter revealed that sequences located approximately 200 bp upstream of the -35 region were required for high-level expression. Removal of these sequences resulted in a 10-fold decline of phi(proV-lacZ)(Hyb2) expression. Osmotic regulation was retained in deletion constructs carrying just 19 bp of chromosomal DNA 5' of the promoter, showing that no sequences further upstream are required for the proper osmoregulation of proU transcription. Experiments with himA and fis mutant strains indicated that the IHF and FIS proteins are not required for the normal osmoregulation of proU expression.
Coinductive Foundations of Infinitary Rewriting and Infinitary Equational Logic

We present a coinductive framework for defining and reasoning about the infinitary analogues of equational logic and term rewriting in a uniform, coinductive way. The setup captures rewrite sequences of arbitrary ordinal length, but it has neither the need for ordinals nor for metric convergence. This makes the framework especially suitable for formalizations in theorem provers.
Visual adaptations in the night‐active wasp Apoica pallens

The apposition compound eye of the nocturnal polistine wasp Apoica pallens shows, in comparison to the closely related diurnal wasp Polistes occidentalis, specific adaptations to vision at low light intensities. When considering recent work on nocturnal and diurnal bees, general principles for dim‐light vision in hymenopterans become evident: The rhabdom diameters in nocturnal bees and wasps are 4 times wider compared to their diurnal relatives, leading to wide receptive fields, which in turn account for a 25‐fold higher optical sensitivity. Interestingly, the rhabdom diameters in both nocturnal bees and wasps measure 8 μm, which may represent the maximum width for nocturnal hymenopteran apposition eyes. A ratio of 1.8 times larger eyes is present in the nocturnal bees and wasps, which in A. pallens is achieved by increasing the facet number, instead of enlarging the facets, as in nocturnal bees. Although this initially indicates spatial resolution to be important for the nocturnal wasp, the wide receptive fields of the rhabdoms will reduce its potentially high acuity. As the optical sensitivity alone cannot account for the 8 log units intensity difference between day and night, a possible role of neural summation within the first optic ganglion (lamina) of nocturnal hymenopterans is discussed. J. Comp. Neurol. 495:255–262, 2006. © 2006 Wiley‐Liss, Inc.