Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical CT-based calculations of dose and positron emitter distributions in proton therapy using the FLUKA Monte Carlo code

Clinical investigations on post-irradiation PET/CT (positron emission tomography/computed tomography) imaging for in vivo verification of treatment delivery and, in particular, beam range in proton therapy are underway at Massachusetts General Hospital (MGH). Within this project, we have developed a Monte Carlo framework for CT-based calculation of dose and irradiation-induced positron emitter distributions. Initial proton beam information is provided by a separate Geant4 Monte Carlo simulation modelling the treatment head. Particle transport in the patient is performed in the CT voxel geometry using the FLUKA Monte Carlo code. The implementation uses a discrete number of different tissue types with composition and mean density deduced from the CT scan. Scaling factors are introduced to account for the continuous Hounsfield unit dependence of the mass density and of the relative stopping power ratio to water used by the treatment planning system (XiO (Computerized Medical Systems Inc.)). Resulting Monte Carlo dose distributions are generally found in good correspondence with calculations of the treatment planning program, except a few cases (e.g. in the presence of air/tissue interfaces). Whereas dose is computed using standard FLUKA utilities, positron emitter distributions are calculated by internally combining proton fluence with experimental and evaluated cross-sections yielding 11C, 15O, 14O, 13N, 38K and 30P. Simulated positron emitter distributions yield PET images in good agreement with measurements. In this paper, we describe in detail the specific implementation of the FLUKA calculation framework, which may be easily adapted to handle arbitrary phase spaces of proton beams delivered by other facilities or include more reaction channels based on additional cross-section data. Further, we demonstrate the effects of different acquisition time regimes (e.g., PET imaging during or after irradiation) on the intensity and spatial distribution of the irradiation-induced β+-activity signal for the cases of head and neck and para-spinal tumour sites.
Ruminal degradability of 15N labelled ribonucleic acid in grass

The ruminal degradation of RNA in rye grass (Lolium perenne) was studied using the bag method. A non-lactating cow (BW 550 kg) fitted with a rumen cannula was used and fed twice daily at maintenance level with a chopped grass hay-based ration containing 30% ground barley. Rye grass, labelled during growth by fertilization with 15N2-urea (9.5 atom% 15N, 20 g N/m2), was cut at seven stages of growth and maturity and freeze-dried. RNA-N represented 6 to 17% of total N. Labelled grass samples (milled to 5.0 mm screen, 5.0 ± 0.1 g DM) were incubated in polyester bags (100 × 200 mm, pore size 50 μm) in the rumen for periods of 1, 3, 6, 9, 12, 24, and 48 h. Data of N and RNA disappearances from the bags were fitted to an exponential equation to estimate parameters of degradation. The effective degradability of RNA in the rumen averaged 90 ± 4%, for N it was 11% units lower (P < 0.001). Degradability of RNA was correlated to that of N (R 2 = 0.92). Degradability of RNA (R 2 = 0.96) and N (R 2 = 0.93) decreased with increasing fibre content of grass. Increasing the fibre content by 1% diminished the degradability of RNA and N by 1.1% units and 2.4% units, respectively (P < 0.001). Assuming a microbial protein synthesis in the rumen of 150 g/kg DOM, a N : RNA ratio of 1 : 1.35 in rumen microbes and a rumen outflow rate of 0.06 h − 1, a model calculation indicates that about 9 to 19% of duodenal RNA are of dietary origin in animals fed grass. This should be taken into account for the calculation of microbial N on the basis of RNA as marker.
Esterase Polymorphism in Camel (Camelus dromedarius) Tissues and Comparison with other Mammalian Species

The activity of carboxyl esterase (CE) and the distribution of esterase isozymes in camel, cow, goat, rabbit, rat, and sheep tissue aqueous extracts were examined using methyl butyrate (MB) as substrate for measuring activity and non denaturant polyacrylamide gel stain after electrophoresis (PAGE) using α-naphthyl acetate (NA) as the substrate. The order of esterase activity was liver > lung > kidney > third stomach > intestine > spleen > heart > plasma > red blood cells. Camel tissues: heart, intestine, kidney, liver, lung, spleen, and stomach exhibited esterase specific activity (ESA) for MB, in μmol/min/g wet tissue, as: 0.67, 2.28, 4.61, 146.0, 29.2, 1.18, and 2.58, respectively. The esterase activity in these tissue extracts exhibited on the gel 3, 5, 1, 3, 2, 3, and 6 bands, respectively. Camel RBC and blood plasma showed no activity in gel electrophoresis. However, camel blood plasma yielded ESA of 0.42 using MB as substrate. Therefore it is concluded that camel serum albumin completely lacks serum esterase-like activity. The range of ESA values in tissue extracts of cow, goat, rabbit, rat, and sheep are as lowest to highest: Heart, 2.26 in goat to 3.75 in rabbit; intestine, 1.46 in cow to 12.8 in rat; kidney, 1.45 in cow to 14.6 in rabbit; liver, 73.4 in cow to 343 in rabbit; lung, 1.35 in goat to 14.6 in rat; spleen, 2.54 in cow to 3.44 in rat; stomach, 1.37 in cow to 3.13 in goat; RBC, 0 in all; plasma, 0.64 in cow to 3.99 in rat. The number of activity bands on the gel by each tissue ranged from one for cow kidney and spleen to nine for sheep intestine and stomach. Keyworda: Camel esterase, camel esterase polymorphism, esterase polymorphism, mammalian esterase, mammalian esterase polymorphism, esterase distribution in mammalian tissues.
Nuclear factor– (cid:1) B and STAT3 are constitutively active in CD138 (cid:2) cells derived from multiple myeloma patients, and suppression of these transcription factors leads to apoptosis

Chemoresistance is a major problem in the treatment of patients with multiple myeloma (MM). Because of the central role of the nuclear transcription factors nuclear factor– (cid:1) B (NF- (cid:1) B) and signal transducer and activator of transcription 3 (STAT3) in chemoresistance, cell survival, and proliferation, we investigated whether MM cells derived from patients express activated NF- (cid:1) B and STAT3 and if their suppression induces apoptosis. We assayed CD138 (cid:2) cells from the bone marrow of 22 MM patients and checked for the activated forms of NF- (cid:1) B and STAT3 by immunocytochemistry. We found that MM cells from all the patients expressed the activated forms of NF- (cid:1) B and STAT3 but to a variable degree (NF- (cid:1) B: low, 3 of 22; moderate, 5 of 22; or high, 14 of 22; STAT3: none, 1 of 22; low, 3 of 22; moderate, 5 of 22; or high, 14 of 22). Constitutive activation of NF- (cid:1) B was in some cases also independently conﬁrmed by electrophoretic mobility gel shift assay. In con-trast to MM patients, activated forms of NF- (cid:1) B and STAT3 were absent in cells from healthy individuals. Suppression of NF- (cid:1) B and STAT3 activation in MM cells by ex vivo treatment with curcumin (diferuloylmethane) resulted in a decrease in adhesion to bone marrow stromal cells, cytokine secretion, and in the viability of cells. When compared with curcumin, dexamethasone was less effective in suppression of NF- (cid:1) B activation and induction of apoptosis in myeloma cells. Overall, our results indicate that fresh cells from MM patients express constitutively active NF- (cid:1) B and STAT3, and suppression of these transcription factors inhibits the survival of the cells. (Blood. 2004;103:3175-3184)
Quantitative gene expression profiling of CD45+ and CD45− skeletal muscle‐derived side population cells

The skeletal muscle‐derived side population (mSP) which highly excludes Hoechst 33342 is composed of CD45+ and CD45− subpopulations; yet, rareness of mSP cells in general has complicated extensive quantitative analysis of gene expression profiles in primarily isolated mSP cells. Here, we describe the isolation of adult mouse normal skeletal muscle residing SPCD45+ and SPCD45− cells from a parent mononuclear muscle‐derived cell (MDC) population. Relative quantitative real time PCR (RT‐PCR) of 64 genes revealed that mSPCD45− compared with mSPCD45+ was enriched for cells expressing transcripts associated with endothelial cells, Notch signaling and myogenic precursors. By comparing the mRNA signatures of mSPs with those of adipose tissue‐derived SP populations, a common endothelial component seemed to reside in both muscle and fat‐derived SPCD45− entities. However, each SP subset was clearly specified by the tissue from which the cells originated suggesting that muscle SPs compared with adipose tissue SPs are predisposed towards differentiation into the myogenic lineage. Thus, our data support the previously suggested hypothesis that satellite cell precursors (or alternatively a satellite cell subpopulation) remain in the mSPCD45− fraction, and we show that these cells express high levels of many of the known myogenic precursor/stem cell related markers, including Pax7 and Myf5. © 2011 International Society for Advancement of Cytometry
Immunoassay of endogenous plasma insulin in man.

For years investigators have sought an assay for insulin which would combine virtually absolute specificity with a high degree of sensitivity, sufficiently exquisite for measurement of the minute insulin concentrations usually present in the circulation. Methods in use recently depend on the ability of insulin to exert an effect on the metabolism of glucose in vivo or in excised muscle or adipose tissue. Thus, the insulin concentration in plasma has been estimated: a) from the degree of hypoglycemia produced in hypophysectomized, adrenalectomized, alloxan-diabetic rats (1); b) from the augmentation of glucose uptake by isolated rat hemidiaphragm (2); or c) from the increased oxidation of glucose-1-C14 by the rat epididymal fat pad (3). Since there have been reports indicating the presence, in plasma, of inhibitors of insulin action (4) and of noninsulin substances capable of inducing an insulin-like effect (5,6), these procedures, while yielding interesting information regarding the effects of various plasmas on glucose metabolism in tissues, are of doubtful specificity for the measurement of insulin per se (5).
Secure speech communication algorithm via DCT and TD-ERCS chaotic map

Secure communication has always been a demanding area in civil, commercial and particularly in military set up. Robust and time-tested efficient algorithms are needed to have an essential privacy for speech transmission in the telephone networks, radio communication and in the emerging cellular mobile radio systems. In this paper, we present a highly secure speech encryption algorithm based on amplitude scrambling and Discrete Cosine Transform (DCT) coefficients scrambling. The permutation is performed using TD-ERCS chaotic map. The proposed scheme has been implemented successfully on software framework which yielded zero residual intelligibility and high quality of recovered speech. Simulation results reveal that the anticipated algorithm is secure enough and resistant against various security attacks. The authors are reasonably confident of their contribution which can eventually be exploited as software, hardware-software and an integral part of any embedded secure communication system.
MDMA and fenfluramine reduce L‐DOPA‐induced dyskinesia via indirect 5‐HT1A receptor stimulation

Chronic l‐3,4‐dihydroxyphenylalanine (L‐DOPA) pharmacotherapy in Parkinson's disease is often accompanied by the development of abnormal and excessive movements known as dyskinesia. Clinical and experimental studies indicate that indirect serotonin agonists can suppress dyskinesia without affecting the efficacy of L‐DOPA. While the mechanism by which these effects occur is not clear, recent research suggests that serotonin 5‐HT1A receptors may play a pivotal role. To test this, male Sprague–Dawley rats with unilateral 6‐hydroxydopamine medial forebrain bundle lesions received 1 week of daily treatment with L‐DOPA (12 mg/kg, i.p.) plus benserazide (15 mg/kg, i.p.). Beginning on the 8th day of treatment and every 3rd or 4th day thereafter, rats were pretreated with vehicle (0.9% NaCl), the serotonin and dopamine releaser 3,4‐methylenedioxymethamphetamine (MDMA; 0.25 or 2.5 mg/kg, i.p.) or the serotonin releaser fenfluramine (FEN; 0.25 or 2.5 mg/kg, i.p.) 5 min prior to L‐DOPA, after which abnormal involuntary movements (AIMs) and rotations were quantified every 20th minute for 2 h. Pretreatment with 2.5 mg/kg of either MDMA or FEN reduced AIMs. To determine the contribution of the 5‐HT1A receptor to these effects, another group of L‐DOPA‐primed 6‐hydroxydopamine‐lesioned rats were pretreated with the 5‐HT1A antagonist WAY100635 (0.5 mg/kg, i.p.), MDMA + WAY100635 (2.5 + 0.5 mg/kg, i.p.) or FEN + WAY100635 (2.5 + 0.5 mg/kg, i.p.) 5 min prior to L‐DOPA and subsequent AIMs and rotation tests. The antidyskinetic effects of MDMA and FEN were reversed by cotreatment with WAY100635. These results suggest that 5‐HT‐augmenting compounds such as MDMA and FEN probably convey antidyskinetic properties in part via stimulation of 5‐HT1A receptors.
Modeling and characterization of InAs/GaAs quantum dot lasers grown using metal organic chemical vapor deposition

We report on the lasing characteristics of three- and five-stack InAs∕GaAs quantum dot (QD) lasers grown by metal organic chemical vapor deposition. By increasing the number of stacked dot layers to 5, lasing was achieved from the ground state at 1135nm for device lengths as short as 1.5mm (no reflectivity coatings). The unamplified spontaneous emission and Z ratio as a function of injection current were also investigated. While the five-stack QD lasers behaved as expected with Z ratios of ≈2 prior to lasing, the three-stack QD lasers, which lased from the excited state, exhibited Z-ratio values as high as 4. A simple model was developed and indicated that high Z ratios can be generated by three nonradiative recombination pathways: (i) high monomolecular recombination within the wetting layer, (ii) Auger recombination involving carriers within the QDs (“unmixed” Auger), and (iii) Auger recombination involving both the QD and wetting layer states (“mixed” Auger), which dominate once the excited and wetting.
The Role of Phonetic Jan P . H . van Sa

This paper addresses three interrelated, broad questions: (i) What type of phonetic knowledge is used in text-to-speech synthesis? (ii) What good does it do? (iii) What future phonetics research does synthesis need? We argue that, depending on the specific architecture and aim of the system (i.e., open domain or closed domain), text-to-speech synthesis systems can incorporate a great variety of facts about human language. These facts do not necessarily take the form of manually crafted rule systems. These rules systems have often have been faulted for fragility, which in turn has been used as an argument for doing away with the incorporation of phonetic knowledge and using machine learning instead. The key importance of incorporating phonetic knowledge is its domain-independence, which lessens the dependence of a system’s performance on the non-generalizable peculiarities of a training corpus. Moreover, current phonetic knowledge is not enough – needed improvements of speech synthesis quality need answers to many general phonetic questions; some examples of these will be provided. For this, however, closer cooperation is needed between the speech technology and phonetics communities.
Internet based teleoperation using wave variables with prediction

Wave-based teleoperation has been previously attempted over the Internet, however performance rapidly deteriorates with increasing delay. The paper focuses on the use of a modified Smith predictor, a Kalman filter and an energy regulator to improve the performance of a wave-based teleoperator. This technique is further extended for use over the Internet, where the time delay is varying and unpredictable. It is shown that the resulting system is stable even if there are large uncertainties in the model of the remote system (used in prediction). Successful experimental results using this technique for teleoperation in a master-slave arrangement over the Internet, where the control signal is streamed between Atlanta (Georgia) and Tokyo (Japan), are also given.
Multimodal neuroimaging evidence of alterations in cortical structure and function in HIV‐infected older adults

Combination antiretroviral therapy transformed human immunodefiency virus (HIV)‐infection from a terminal illness to a manageable condition, but these patients remain at a significantly elevated risk of developing cognitive impairments and the mechanisms are not understood. Some previous neuroimaging studies have found hyperactivation in frontoparietal networks of HIV‐infected patients, whereas others reported aberrations restricted to sensory cortices. In this study, we utilize high‐resolution structural and neurophysiological imaging to determine whether alterations in brain structure, function, or both contribute to HIV‐related cognitive impairments. HIV‐infected adults and individually matched controls completed 3‐Tesla structural magnetic resonance imaging (sMRI) and a mechanoreception task during magnetoencephalography (MEG). MEG data were examined using advanced beamforming methods, and sMRI data were analyzed using the latest voxel‐based morphometry methods with DARTEL. We found significantly reduced theta responses in the postcentral gyrus and increased alpha activity in the prefrontal cortices of HIV‐infected patients compared with controls. Patients also had reduced gray matter volume in the postcentral gyrus, parahippocampal gyrus, and other regions. Importantly, reduced gray matter volume in the left postcentral gyrus was spatially coincident with abnormal MEG responses in HIV‐infected patients. Finally, left prefrontal and postcentral gyrus activity was correlated with neuropsychological performance and, when used in conjunction, these two MEG findings had a sensitivity and specificity of over 87.5% for HIV‐associated cognitive impairment. This study is the first to demonstrate abnormally increased activity in association cortices with simultaneously decreased activity in sensory areas. These MEG findings had excellent sensitivity and specificity for HIV‐associated cognitive impairment, and may hold promise as a potential disease marker. Hum Brain Mapp 36:897–910, 2015. © 2014 Wiley Periodicals, Inc.
Atmospheric Longwave Infrared Emission Spectroscopy of Water Vapor at the South Pole

The downward infrared radiance spectrum was measured with a Michelson Long Wave Infrared (LWIR) spectrometer at the Amundsen-Scott South Pole Station. Spectra were collected year-round at the South Pole in 1998. This research focuses on the atmospheric water emission lines between 250 and 800 cm -1 (40 to 12.5 μm) region. The spectral resolution is 1 cm -1 . The atmosphere over the South Pole is the driest and coldest on Earth. Winter surface temperatures average approximately -60°C, while the total column water vapor is about 300 μm of precipitable water. Measured clear sky cases were selected for summer and winter months to represent and investigate water in the seasonal extremes. The LWIR spectra are modeled using the Line-By-Line Radiative Transfer Model (LBLRTM) software, the HITRAN database, and NMC temperature and pressure profiles. These spectra are then fitted as closely as possible to the measured spectra to retrieve water column amounts, and to obtain other important information about the atmosphere.
Assessment of coronary artery calcium by chest CT compared with EKG-gated cardiac CT in the multicenter AIDS cohort study

Rationale Individuals with HIV are at increased risk for coronary artery disease (CAD). Early detection of subclinical CAD by assessment of coronary artery calcium (CAC) may help risk stratify and prevent CAD events in these individuals. However, the current standard to quantify CAC i.e. Agatston scoring requires EKG-gated cardiac CT imaging. Objective To determine if the assessment of CAC using non-EKG-gated chest CT and the Weston scoring system is a useful surrogate for Agatston scores in HIV-infected and HIV-uninfected individuals. Methods and measurements CAC was assessed by both the Weston and Agatston score in 108 men enrolled in the Multicenter AIDS Cohort Study. Results Participants were 55.2 (IQR 50.4; 59.9) years old and 62 (57.4%) were seropositive for HIV. Inter-observer agreement (rs = 0.94, κ = 90.0%, p<0.001, n = 21) and intra-observer agreement (rs = 0.95, κ = 95.2%, p<0.001, n = 97) for category of Weston score were excellent. Weston scores were associated with similar CAD risk factors as Agatston scores (age, race, HDL cholesterol level, all p<0.05) in our cohort. There was excellent correlation (rs = 0.92, p<0.001) and agreement (κw = 0.77, p<0.001) between Weston and Agatston scores. Conclusions This study is the first to examine calcium scoring using chest CT in HIV-infected individuals and to independently validate the Weston score as a surrogate for the Agatston score. In clinical or research settings where EKG-gated cardiac CT is not feasible for the assessment of coronary calcium, Weston scoring by using chest CT should be considered.
Cytosolic PINK1 promotes the targeting of ubiquitinated proteins to the aggresome-autophagy pathway during proteasomal stress

ABSTRACT During proteasomal stress, cells can alleviate the accumulation of polyubiquitinated proteins by targeting them to perinuclear aggresomes for autophagic degradation, but the mechanism underlying the activation of this compensatory pathway remains unclear. Here we report that PINK1-s, a short form of Parkinson disease (PD)-related protein kinase PINK1 (PTEN induced putative kinase 1), is a major regulator of aggresome formation. PINK1-s is extremely unstable due to its recognition by the N-end rule pathway, and tends to accumulate in the cytosol during proteasomal stress. Overexpression of PINK1-s induces aggresome formation in cells with normal proteasomal activities, while loss of PINK1-s function leads to a significant decrease in the efficiency of aggresome formation induced by proteasomal inhibition. PINK1-s exerts its effect through phosphorylation of the ubiquitin-binding protein SQSTM1 (sequestosome 1) and increasing its ability to sequester polyubiquitinated proteins into aggresomes. These findings pinpoint PINK1-s as a sensor of proteasomal activities that transduces the proteasomal impairment signal to the aggresome formation machinery.
In Vivo Internalization of the Somatostatin sst2A Receptor in Rat Brain: Evidence for Translocation of Cell-Surface Receptors into the Endosomal Recycling Pathway

To determine whether cellular compartmentalization of somatostatin receptors can be regulated in vivo, we examined the immunocytochemical distribution of the sst2A receptor (sst2AR) after stereotaxical injections of somatostatin analogs into the rat parietal cortex. Whereas CH-275, a sst1R agonist, failed to induce changes in the diffuse sst2AR immunostaining pattern characteristic of control animals, somatodendritic profiles displaying intracytoplasmic immunoreactive granules became apparent short-term after injection of either somatostatin or the sst2R agonist octreotide. Confocal microscopy revealed that 90% of sst2AR-immunoreactive endosome-like organelles displayed transferrin receptor immunoreactivity. At the electron microscopic level, the percentage of sst2AR immunoparticles dramatically decreased at the plasmalemma of perikarya and dendrites after octreotide injection. Conversely, it significantly increased in endosomes-like organelles. These results demonstrate that sst2ARs undergo, in vivo, rapid and massive internalization into the endocytic recycling compartment in response to acute agonist stimulation and provide important clues toward elucidating somatostatin receptor signaling in the mammalian brain.