Miracle-dz/UniFAR-FTUs huggingface dataset:
Acute phase response impairs host defense against Pseudomonas aeruginosa pneumonia in mice*

Objective: Pseudomonas aeruginosa is a common pathogen in hospital-acquired pneumonia. Especially trauma and postsurgical patients display a profound acute phase protein response and are susceptible to acquiring pneumonia. The objective was to study the influence of the acute phase response induced by sterile tissue injury on pulmonary host defense. Design: Laboratory investigation. Setting: Academic medical center. Subjects: Female C57Bl/6 wild-type mice, 8–10 wks old. Interventions: Mice were injected subcutaneously with either turpentine or sterile saline (control) in both hind limbs 1 day before intranasal infection with P. aeruginosa. Measurements and Main Results: The turpentine-induced acute phase response was associated with 100% lethality after induction of pneumonia, whereas control mice all survived the Pseudomonas infection. In addition, turpentine-injected mice demonstrated much higher bacterial loads in their lungs and an increased dissemination of the infection. The acute phase reaction attenuated lung inflammation during pneumonia, as reflected by histopathology, reduced pulmonary levels of proinflammatory cytokines, and a strongly diminished recruitment of neutrophils to the site of infection. Blood neutrophils harvested from turpentine injected mice displayed a reduced capacity to up-regulate their CD11b/CD18 expression upon stimulation with Pseudomonas ex vivo and during Pseudomonas pneumonia in vivo. Administration of a blocking anti-CD11b antibody to turpentine-injected and control mice almost completely abrogated the difference in bacterial outgrowth, whereas inhibition of the sympathetic nervous system did not affect the impaired pulmonary host defense in mice with an acute phase response. Conclusions: These data suggest that a systemic acute phase response might impair host defense against P. aeruginosa pneumonia, possibly in part by inhibition of CD11b/CD18-dependent neutrophil recruitment.
Immunohistochemical Analysis of the Proteolytic Enzyme Subtilase in the Digestive Organs of the Sea Urchin Strongylocentrotus intermedius

Subtilase, a major protease in the short‐spined sea urchin (Strongylocentrotus intermedius), was isolated and used as antigen for the subsequent production of a specific polyclonal antibody. Immunoreactive cells were observed by immunohistochemical analysis in granules in the anterior and posterior stomach and the anterior intestine. These granules, which were most numerous in the anterior stomach, also stained intensely with methylene blue‐Azure II. However, granules in cells of the esophagus, posterior intestine, and rectum were not stained by this antibody. We conclude that subtilase mainly localizes in the stomach and anterior intestine of the sea urchin. Anat Rec, 2012. © 2011 Wiley Periodicals, Inc.
A molecular dynamics approach to study the importance of solvent in protein interactions

Water constitutes the cellular environment for biomolecules to interact. Solvent is important for protein folding and stability, and it is also known to actively participate in many catalytic processes in the cell. However, solvent is often ignored in molecular recognition and not taken into account in protein–protein interaction studies and rational design. Previously we developed SCOWLP, a database and its web application (http://www.scowlp.org), to perform studies on the contribution of solvent to protein interface definition in all protein complexes of the PDB. We introduced the concept of wet spots, interfacial residues interacting only through one water molecule, which were shown to considerably enrich protein interface descriptions. Analysis of interfacial solvent in a nonredundant dataset of protein complexes suggested the importance of including interfacial water molecules in protein interaction studies. In this work we use a molecular dynamics approach to gain deeper insights into solvent contribution to protein interfaces. We characterize the dynamic and energetic properties of water‐mediated protein interactions by comparing different interfacial interaction types (direct, dual and wet spot) at residue and solvent level. For this purpose, we perform an analysis of 17 representative complexes from two protein families of different interface nature. Energetically wet spots are quantitatively comparable to other residues in interfaces, and their mobility is shown to be lower than protein surface residues. The residence time of water molecules in wet spots sites is higher than of those on the surface of the protein. In terms of free energy, though wet‐spots‐forming water molecules are very heterogeneous, their contribution to the free energy of complex formation is considerable. We find that water molecules can play an important role in interaction conservation in protein interfaces by allowing sequence variability in the corresponding binding partner, and we discuss the important implications of our observations related to the use of the correlated mutations concept in protein interactions studies. The results obtained in this work help to deepen our understanding of the physico–chemical nature underlying protein–protein interactions and strengthen the idea of using the wet spots concept to qualitatively improve the accuracy of folding, docking and rational design algorithms. Proteins 2008. © 2008 Wiley‐Liss, Inc.
A boundary element procedure for contact problems in plane linear elastostatics

Nous presentons un nouveau procede d'approximation pour resoudre des problemes de contact en elastostatique lineaire plane. En utilisant la methode integrale, nous obtenons une inequation variationnelle ayant comme inconnues la trace du champ des deplacements et le vecteur des contraintes aux limites. Notre travail couvre le cas des problemes meles avec des conditions aux limites du type Neumann et du type Signorini sans imposer aux deplacements d'avoir lieu dans une partie de la frontiere du corps elastiquement deforme. Sans avoir besoin d'une hypothese de regularite, nous etablissons la convergence en norme des approximations pour des elements de frontiere polynomiaux par morceaux
The effect of short-term dimethylglycine treatment on oxygen consumption in cytochrome oxidase deficiency: a double-blind randomized crossover clinical trial.

OBJECTIVE To study the effectiveness of dimethylglycine (DMG) on oxygen consumption (VO(2)) in children with Saguenay-Lac-Saint-Jean cytochrome-c oxidase (SLSJ-COX) deficiency (OMIM 220111). STUDY DESIGN In a crossover randomized double-blind clinical trial, 5 children with SLSJ-COX deficiency, who were stable and old enough to comply with VO(2) measurement, were treated with placebo or DMG for 3 days, and with the alternate treatment after a 2-week washout period. VO(2) was measured by indirect calorimetry before and after treatment. Dietary caloric intake was calculated for 3 days before each measurement. Mean caloric intakes per day were 1562 and 1342 kcal x m(-2) before and during placebo, 1,336 and 1,380 before and during DMG, respectively. RESULTS DMG was well tolerated and, in all cases, resulted in markedly increased blood DMG levels (617 + 203 mmol x L(-1)), versus 0 to 2 mmol x L(-1) without treatment. Mean VO(2) was lower after administration of either DMG (-1 +/- 3 mL x min(-1) x m(-2)) or placebo (-6 +/- 4), but neither difference was statistically significant. There was no detectable effect of DMG treatment on blood levels of lactate, pyruvate, bicarbonate, or pH. VO(2) values of patients (range, 101-135 mL x min(-1) x m(-2)) were lower than published norms (150-160 mL x min(-1) x m(-2)). CONCLUSION This study suggests that treatment with DMG does not substantially change VO(2) in children with SLSJ-COX deficiency.
Efficacy and safety of infrared warming of the eyelids.

PURPOSE To evaluate our newly developed infrared heater (IRH) and compare it to a broad-spectrum heater (BSH) for warming the eyelids. MATERIALS AND METHODS Ten normal subjects were enrolled in this study. All measurements were recorded in a room with temperature 23 degrees C, 40% humidity, and no wind. The IRH is composed of two hard eye patches that have light-emitting diodes (LEDs) emitting near-infrared radiation. We first compared the temperature rises in the cornea, lacrimal gland, and eyelids after warming through closed eyelids with the IRH for 5 and 10 min. Next, we compared warming with the IRH or BSH for 30 min. We then used the IRH for 5 min with the eyes open to confirm its safety. Finally, we determined subjective feeling after warming the eyes. RESULTS Direct comparison of 5 versus 10 min of warming with the IRH showed no significant differences in temperature rises in the upper eyelid (p = 0.09). The IRH caused significantly more heating (p < 0.05) than did the BSH everywhere except the cornea. The temperatures never rose above 37.7 degrees C for either heater during 30 min or with the IRH with the eyes open for 5 min. The subjects' comfort level rose significantly (p < 0.05) after treatment with the IRH. CONCLUSIONS Our study showed the efficacy and safety of warming the eyelids with a newly developed IRH. Only 5 min is necessary to increase ocular temperature and enhance comfort.
An Assistive Image-Guided Surgical Robot System Using O-Arm Fluoroscopy for Pedicle Screw Insertion: Preliminary and Cadaveric Study

BACKGROUND: The biplane fluoroscopy guided robot system (BFRS) was developed for surgical robotic systems, minimally invasive surgeries, and cooperative robotic systems, as well as enhanced surgical planning and navigation with preoperative and intraoperative image data. OBJECTIVE: To propose a novel surgical robot system for percutaneous pedicle screw insertion. METHODS: The BFRS consists of an O-shaped biplane fluoroscope (O-arm), a surgical planning and operating system, and an assistive robot. Each part of the BFRS has a role in conducting percutaneous pedicle screw placements. To evaluate BFRS accuracy, each part was analyzed, and to assess the safety and feasibility of percutaneous pedicle screw insertions with the BFRS, cadaveric studies involving 14 levels in the thoracic and lumbar spine regions were conducted on 2 cadavers. RESULTS: Errors in each part of the system and within the entire system were evaluated. The accuracy of generating coordinates using O-arm images was 0.30 ± 0.15 mm. The robot demonstrated a duplication value of 4.97 μm RMS and an accuracy of 0.358 mm RMS. Total system error was 1.38 ± 0.21 mm. The results of the cadaveric studies show that inserted pedicular screws were adequately located within the spine with no unexpected malpositioning of the screws. The axial angle difference between planned and postoperative data was 2.45 ± 2.56°, and the sagittal angle difference was 0.71 ± 1.21°. CONCLUSION: The BFRS might be helpful in improving the accuracy of percutaneous pedicular screw insertion procedures. In the future, we will attempt to improve the accuracy and reliability of the BFRS and to determine new clinical applications for the BFRS.
Emotion recognition in audio records

A novel approach to find the combination of acoustic features producing a more robust automatic recognition of a speaker emotion is proposed. Four discrete emotional states are classified. The emotional speech corpora used for training and evaluation are described in detail. The emotion recognition model using acoustic features is presented. The results achieved are presented and discussed.
A novel silicon "star-comb" microphone concept for enhanced signal-to-noise-ratio: Modeling, design and first prototype

A novel comb-structure-based, capacitive MEMS microphone concept is proposed, which is expected to significantly reduce viscous damping losses, challenging the high performance of conventional MEMS microphones. To this end, we derived a dedicated, fully energy-coupled and properly calibrated system-level model scaling with all relevant design parameters. It enables to discriminate in detail the impact of the individual components like transducer, package and electrostatic read out to the overall signal-to-noise-ratio (SNR) of the microphone and hence, to identify the optimal design of the device. Measurements of first prototypes show promising results and agree very well with simulations demonstrating the predictive power of the model w.r. t. to further optimization.
Arm and shoulder morbidity in breast cancer patients after breast-conserving therapy versus mastectomy

Introduction. The objective of this study was to compare the prevalence of late effects in the arm and shoulder in patients with breast cancer stage II who had radical modified mastectomy (RM) or breast-conserving therapy (BCT) followed by loco-regional adjuvant radiotherapy with or without chemotherapy/anti-oestrogen. Material and methods. All patients had axillary lymph node dissection. At a median of 47 months (range 32–87) post-surgery, 263 women (RM: n=186, BCT: n=77) were seen during an outpatient visit and had their arm and shoulder function and the presence of lymphedema assessed by a clinical examination, interview and self-rating. Volume calculation was used to measure lymphedema. Results. In the RM group 20% had developed arm lymphedema versus 8% in the BCT group (p=0.02). In multivariate analysis lymphedema was associated with a higher number of metastatic axillary lymph nodes [OR1.14, p=0.02], RM [OR 2.75, p=0.04] and increasing body mass index (BMI) [OR 1.11, p<0.01]. In the RM group 24% had a restricted range of motion in shoulder flexion compared to 7% in the BCT group (p<0.01). Shoulder pain was reported by 32% in the RM group and by 12% in the BCT group (p=0.001). Increasing observation time, RM, and increasing BMI were significantly associated with impaired arm/shoulder function. Discussion. Arm/shoulder problems including lymphedema were significantly more common after RM compared to BCT in irradiated breast cancer patients who have undergone axillary lymph node dissection. The performance of BCT should be encouraged when appropriate, to ensure a low prevalence of arm/shoulder morbidity including lymphedema.
Testing quantum adiabaticity with quench echo

Adiabaticity of quantum evolution is important in many settings; one example is adiabatic quantum computation (AQC). Nevertheless, to date, there is no effective method available for testing the adiabaticity of the evolution for the case where the eigenenergies of the driven Hamiltonian are not known. We propose a simple method for checking the adiabaticity of a quantum process for an arbitrary quantum system. We further propose an operational method for finding more efficient protocols that approximate adiabaticity, and suggest a ‘uniformly adiabatic’ quench scheme based on the Kibble–Zurek mechanism for the case where the initial and final Hamiltonians are given. This method should help in implementing AQC and other tasks where preserving the system in the ground state of a time-dependent Hamiltonian is desired.
Toward a molecular programming language for algorithmic self-assembly

Self-assembly is the process whereby relatively simple components autonomously combine to form more complex objects. Nature exhibits self-assembly to form everything from microscopic crystals to living cells to galaxies. With a desire to both form increasingly sophisticated products and to understand the basic components of living systems, scientists have developed and studied artificial self-assembling systems. One such framework is the Tile Assembly Model introduced by Erik Winfree in 1998. In this model, simple two-dimensional square ‘tiles’ are designed so that they self-assemble into desired shapes. The work in this thesis consists of a series of results which build toward the future goal of designing an abstracted, highlevel programming language for designing the molecular components of self-assembling systems which can perform powerful computations and form into intricate structures. The first two sets of results demonstrate self-assembling systems which perform infinite series of computations that characterize computably enumerable and decidable languages, and exhibit tools for algorithmically generating the necessary sets of tiles. In the next chapter, methods for generating tile sets which self-assemble into complicated shapes, namely a class of discrete self-similar fractal structures, are presented. Next, a software package for graphically designing tile sets, simulating their self-assembly, and debugging designed systems is discussed. Finally, a high-level programming language which abstracts much of the complexity and tedium of designing such systems, while preventing many of the common errors, is presented. The summation of this body of work presents a broad coverage of the spectrum of desired outputs from artificial self-assembling systems and a progression in the sophistication of tools used to design them. By creating a broader and deeper set of modular tools for designing xii self-assembling systems, we hope to increase the complexity which is attainable. These tools provide a solid foundation for future work in both the Tile Assembly Model and explorations into more advanced models.
Comparative Diagnostic Value of Ankle-to-Brachial Index and Transcutaneous Oxygen Tension at Rest and After Exercise in Patients with Intermittent Claudication

Background: Few studies have compared sensitivities of ankle-to-brachial index (ABI) and transcutaneous oxygen tension (TcPO2) in a large group of patients with Leriche stage II intermittent claudication. Method and Results: 111 patients (138 limbs) with a stable chronic (> three months) intermittent claudication and significant peripheral vascular disease (PVD) proved by angiography were studied. They performed a treadmill test (10%, 3 km/hr) limited by limb pain. ABI and TcPO2 were measured before, just after exercise, and after three and ten minutes of recovery in supine position. Sensitivities per patient for ABI and TcPO2 were respectively at rest: 82.9% and 28.8%, and after exercise: 88.3% and 62.2%. Sensitivities per leg (n=138) for ABI and TcPO2 were respectively at rest: 73.9% and 26.8%, and after exercise: 82.6% and 34%. The sensitivity of TcPO2 increased to 56.5% after three minutes of recovery but was always less than that of ABI, which was maximal just after exercise (82.6%). The sensi tivity of the regional perfusion index was similar to that of TcPO2. The sensitivity of TcPO2 increased with respect to the Leriche stage and the number of lesions but was always lower than that of ABI. There was a weak correlation between TcPO2 and ABI after exercise, but no correlation was noted between maximal walking distance, ABI, and TcPO2. Conclusion: TcPO 2 is not required in patients with Leriche stage II intermittent clau dication but might be useful either in severely affected patients (Leriche stage III or IV) or in selected patients.
Basal resistance enhances warming tolerance of alien over indigenous species across latitude

Significance How climate change and biological invasions interact to affect biodiversity is of major concern to conservation. Quantitative evidence for the nature of climate change–invasion interactions is, however, limited. For the soil ecosystem fauna, such evidence is nonexistent. Yet across the globe, soil-dwelling animals regulate belowground functioning and have pronounced influences on aboveground dynamics. Using springtails as an exemplar taxon, widely known to have species-specific effects on below- and aboveground dynamics, we show that across a wide latitudinal span (16–54°S), alien species have greater ability to tolerate climate change-associated warming than do their indigenous counterparts. The consequences of such consistent differences are profound given globally significant invasions of soil systems by springtails. Soil systems are being increasingly exposed to the interactive effects of biological invasions and climate change, with rising temperatures expected to benefit alien over indigenous species. We assessed this expectation for an important soil-dwelling group, the springtails, by determining whether alien species show broader thermal tolerance limits and greater tolerance to climate warming than their indigenous counterparts. We found that, from the tropics to the sub-Antarctic, alien species have the broadest thermal tolerances and greatest tolerance to environmental warming. Both groups of species show little phenotypic plasticity or potential for evolutionary change in tolerance to high temperature. These trait differences between alien and indigenous species suggest that biological invasions will exacerbate the impacts of climate change on soil systems, with profound implications for terrestrial ecosystem functioning.
Stabilization of α-Synuclein Secondary Structure upon Binding to Synthetic Membranes*

α-Synuclein is a highly conserved presynaptic protein of unknown function. A mutation in the protein has been causally linked to Parkinson’s disease in humans, and the normal protein is an abundant component of the intraneuronal inclusions (Lewy bodies) characteristic of the disease. α-Synuclein is also the precursor to an intrinsic component of extracellular plaques in Alzheimer’s disease. The α-synuclein sequence is largely composed of degenerate 11-residue repeats reminiscent of the amphipathic α-helical domains of the exchangeable apolipoproteins. We hypothesized that α-synuclein should associate with phospholipid bilayers and that this lipid association should stabilize an α-helical secondary structure in the protein. We report that α-synuclein binds to small unilamellar phospholipid vesicles containing acidic phospholipids, but not to vesicles with a net neutral charge. We further show that the protein associates preferentially with vesicles of smaller diameter (20–25 nm) as opposed to larger (∼125 nm) vesicles. Lipid binding is accompanied by an increase in α-helicity from 3% to approximately 80%. These observations are consistent with a role in vesicle function at the presynaptic terminal.
Pulmonary Reimplantation Response

REIMPLANTATION or autotransplantation of the lung is a formidable procedure involving division of many structures. In the past, reimplantation of the canine lung presented technical problems which resulted in high surgical mortality and appreciable compromise of the bronchial and vascular anastomoses with consequent functional impairments in surviving animals.3'6"11,18,20'24 Recent technical improvements have made it possible to minimize defects at the bronchial and vascular anastomoses;2'22 a reimplanted lung can now recover normal morphology and function remarkably well if the bronchus and major vessels are adequately reconstructed.10'20.23 After technically flawless reimplantation, however, functional defects may occur in the early postoperative period. These defects are largely reversible'3'21 and may be attributed to disruption of nerves, lymphatics and bronchial vessels and/or to ischemic injury.1"7"1'2,8 We have been investigating the mechanisms of pulmonary allograft rejection in dogs using serial chest roentgenography and pulmonary angiography with simultaneous lung biopsy.1'5"6 Serial chest roentgenography is an important means of monitoring the status of the allograft in the postoperative period. Since the anticipated responses to autotransplantation have not been adequately defined, it may be difficult to determine whether a postoperative pulmonary roentgenologic abnormality is due to rejection or reimplantation. The present study was undertaken to allow us to establish
The effect of proton and gamma radiation on different types of temperature sensors

In a study performed to test the effects of proton and gamma radiation on different temperature sensors, Pt RTDs and thermocouples show a negligible sensitivity. On the other hand, IC-based temperature sensors modify significantly their behavior. AD590 sensors exhibit a moderate degradation, depending on the encapsulation. And TMP36 sensors experiment a big degradation amounting up to a change in the readout signal about 20 °C for a total ionizing dose of 40 krad.