Miracle-dz/UniFAR-FTUs huggingface dataset:
PET Monitoring of Therapy Response in Head and Neck Squamous Cell Carcinoma

In the Western world, more than 90% of head and neck cancers are head and neck squamous cell carcinomas (HNSCCs). The most appropriate treatment approach for HNSCC varies with the disease stage and disease site in the head and neck. Concurrent chemoradiotherapy has become a widely used means for the definitive treatment of locoregionally advanced HNSCC. Although this multimodality treatment provides higher response rates than radiotherapy alone, the detection of residual viable tumor after the end of therapy remains an important issue and is one of the major applications of 18F-FDG PET. Studies have shown that negative 18F-FDG PET or PET/CT results after concurrent chemoradiotherapy have a high negative predictive value (>95%), whereas the positive predictive value is only about 50%. However, when applied properly, FDG PET/CT can exclude residual disease in most patients, particularly patients with residual enlarged lymph nodes who would otherwise undergo neck dissection. In contrast to other malignancies, data are limited on the utility of 18F-FDG PET for monitoring the response to induction chemotherapy in HNSCC or for assessing treatment response early during the course of definitive chemoradiotherapy. The proliferation marker 18F-3′-deoxy-3′fluorothymidine is currently under study for this purpose. Beyond standard chemotherapy, newer treatment regimens in HNSCC take advantage of our improved understanding of tumor biology. Two molecules important in the progression of HNSCC are the epidermal growth factor receptor and the vascular endothelial growth factor (VEGF) and its receptor VEGF-R. Drugs attacking these molecules are now under study for HNSCC. PET probes have been developed for imaging the presence of these molecules in HNSCC and their inhibition by specific drug interaction; the relevance of these probes for response assessment in HNSCC will be discussed. Hypoxia is a common phenomenon in HNSCC and renders cancers resistant to chemo- and radiotherapy. Imaging and quantification of hypoxia with PET probes is under study and may become a prerequisite for overcoming chemo- and radioresistance using radiosensitizing drugs or hypoxia-directed irradiation techniques and for monitoring the response to these techniques in selected groups of patients. Although 18F-FDG PET/CT will remain the major clinical tool for monitoring treatment in HNSCC, other PET probes may have a role in identifying patients who are likely to benefit from treatment strategies that include biologic agents such as epidermal growth factor receptor inhibitors or VEGF inhibitors.
Virtual colonoscopy

The book provides precise instructions on how to prepare the patient and specific protocols for the various CT scanners currently in use. Detailed chapters on interpretation demonstrate normal anatomy, anatomic variants, CT appearances of polyps and cancer, and pitfalls of interpretation on two-dimensional and three-dimensional views. Additional chapters cover extracolonic findings, reporting, and fecal and fluid tagging. More than 700 illustrations show examination techniques and normal and pathologic findings.
Layered Decoding of Non-Layered LDPC Codes

The principle of "layered decoding" is extended to those codes not especially conceived for this practice, as to benefit of the increased convergence speed. Two different strategies are considered to solve the problem and the related architectures presented: one more straightforward, and based on the use for the soft output of the last value originated in a layer; the other based on the computation of the variation (or delta) of the soft output metrics to allow concurrent updates. Then, as in architecture-first approach, the performance is assessed for several widths of the layer, which remarks the robustness of the delta-mechanism to high parallelisation factors. As in the exact layered decoding, the average boost of two times in the convergence speed is shown
Changes and tracking of mammographic density in relation to Pike's model of breast tissue aging: a UK longitudinal study

Percent mammographic density (PMD) is a strong marker of breast cancer risk. It may be a correlate of the rate of breast tissue aging, as proposed by Pike to explain breast cancer age‐incidence. We examined longitudinal changes in PMD in 645 breast screening attendees in London, UK, in which each had between 2 and 5 screens spanning 3–12 years at ages 50–65 years and compare these to Pike's model. Within‐woman PMD declined during these ages, with a slowing rate of decline. Annual rates of decline were 1.4% (95% confidence interval: 1.2–1.6), 0.7% (0.6–0.9) and 0.1% (–0.2 to 0.4) at ages 50, 57 and 64. Dense area declined similarly, but the absolute magnitude of the rate of increase of nondense area was almost double that of dense area. PMD dropped by 2.4% (1.4–3.4) on menopausal transition and increased by 2.4% (1.4–3.5) with the use of hormone therapy. Higher body mass index, greater parity and being Afro‐Caribbean or South Asian ethnicities were associated with lower PMD, but did not affect rate of change of PMD at these ages. Within‐woman rank correlation of PMD was 0.80 for readings taken 9 years apart. Effects of menopause and parity and the lack of effect of menarche on age‐specific PMD at these ages are consistent with the predicted determinants in Pike's model. A high degree of tracking of PMD indicates that at ages 50–65 years high‐risk women could be identified by a single early screen at age older than 50.
An Integrated GNSS/INS/LiDAR-SLAM Positioning Method for Highly Accurate Forest Stem Mapping

Forest mapping, one of the main components of performing a forest inventory, is an important driving force in the development of laser scanning. Mobile laser scanning (MLS), in which laser scanners are installed on moving platforms, has been studied as a convenient measurement method for forest mapping in the past several years. Positioning and attitude accuracies are important for forest mapping using MLS systems. Inertial Navigation Systems (INSs) and Global Navigation Satellite Systems (GNSSs) are typical and popular positioning and attitude sensors used in MLS systems. In forest environments, because of the loss of signal due to occlusion and severe multipath effects, the positioning accuracy of GNSS is severely degraded, and even that of GNSS/INS decreases considerably. Light Detection and Ranging (LiDAR)-based Simultaneous Localization and Mapping (SLAM) can achieve higher positioning accuracy in environments containing many features and is commonly implemented in GNSS-denied indoor environments. Forests are different from an indoor environment in that the GNSS signal is available to some extent in a forest. Although the positioning accuracy of GNSS/INS is reduced, estimates of heading angle and velocity can maintain high accurate even with fewer satellites. GNSS/INS and the LiDAR-based SLAM technique can be effectively integrated to form a sustainable, highly accurate positioning and mapping solution for use in forests without additional hardware costs. In this study, information such as heading angles and velocities extracted from a GNSS/INS is utilized to improve the positioning accuracy of the SLAM solution, and two information-aided SLAM methods are proposed. First, a heading angle-aided SLAM (H-aided SLAM) method is proposed that supplies the heading angle from GNSS/INS to SLAM. Field test results show that the horizontal positioning accuracy of an entire trajectory of 800 m is 0.13 m and is significantly improved (by 70%) compared to that of a traditional GNSS/INS; second, a more complex information added SLAM solution that utilizes both heading angle and velocity information simultaneously (HV-aided SLAM) is investigated. Experimental results show that the horizontal positioning accuracy can reach a level of six centimetres with the HV-aided SLAM, which is a significant improvement (by 86%). Thus, a more accurate forest map is obtained by the proposed integrated method.
Arab American Emerging Adults’ Ethnic Identity and Its Relation to Psychological Well-Being

Despite Arab Americans’ increasing population in the United States, there is limited research concerning their psychological functioning. Ethnic identity (EI) has been found to positively predict the psychological well-being of various ethnic minority individuals. Therefore, in a sample of Arab American, emerging adult college students, we investigated how Phinney’s Multigroup EI Measure subscales (i.e., Other-Group Orientation (OGO), Affirmation & Belonging, EI Exploration, and EI Commitment) predicted components of the Ryff Scales of Psychological Well-Being (i.e., Self-Acceptance, Personal Growth, and Purpose in Life). Affirmation & Belonging positively predicted Self-Acceptance, EI Commitment predicted Purpose in Life, and OGO predicted Personal Growth. Additionally, EI Exploration negatively predicted Self-Acceptance. Findings were generally consistent with Social Identity Theory, Erikson’s theory, Phinney’s theory, and previous research. Results demonstrated the importance of studying components of Arab American emerging adults’ EI in relation to under-researched forms of psychological well-being.
Univariate real root isolation in multiple extension fields

We present algorithmic, complexity and implementation results for the problem of isolating the real roots of a univariate polynomial in <i>B</i><sub>α</sub> ∈ <i>L</i>[<i>y</i>], where <i>L</i> = Q(α<sub>1</sub>,., α<sub>ℓ</sub>) is an algebraic extension of the rational numbers. Our bounds are single exponential in ℓ and match the ones presented in [34] for the case ℓ = 1. We consider two approaches. The first, indirect approach, using multivariate resultants, computes a univariate polynomial with integer coefficients, among the real roots of which are the real roots of <i>B</i><sub>α</sub>. The Boolean complexity of this approach is O<sub><i>B</i></sub>(<i>N</i><sup>4ℓ+4</sup>), where <i>N</i> is the maximum of the degrees and the coefficient bitsize of the involved polynomials. The second, direct approach, tries to solve the polynomial directly, without reducing the problem to a univariate one. We present an algorithm that generalizes Sturm algorithm from the univariate case, and modified versions of well known solvers that are either numerical or based on Descartes' rule of sign. We achieve a Boolean complexity of O<sub><i>B</i></sub> [equation], respectively. We implemented the algorithms in C as part of the core library of Mathematica and we illustrate their efficiency over various data sets.
Further Improvements in SOVA for High-Throughput Parallel Turbo Decoding

In this letter, we present two mechanisms based on soft-output Viterbi algorithm (SOVA) technique that achieve a performance close to maximum a posteriori (MAP) decoding. First, we propose a new technique called alternating direction SOVA, which allows for improving the performance of SOVA in similar terms as bidirectional SOVA while barely affecting the area complexity. Then, we introduce the idea of parallel turbo decoding based on path metric/state border exchange. Unlike other techniques, overlapping between adjacent subblocks is not required, thus reducing the decoding latency dramatically. We evaluate their performance in the context of 3GPP-LTE, showing that the combination of both mechanisms achieves a BER performance close to parallel MAP decoding while having a lower complexity.
Spectral decomposition methods for the analysis of MRS information from human brain tumors

The clinical assessment of human brain tumors requires the use of non-invasive information measurement technologies, usually from the modalities of imaging or spectroscopy. The latter may provide insight into the tumor metabolism. The Magnetic Resonance Spectroscopy (MRS) signal is the result of the combination of heterogeneous signal sources. In this study, we investigate the use of two spectral decomposition techniques for the identification of such sources in MRS from brain tumors collected in an international database, and for a number of different diagnostic problems.
Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database.

BACKGROUND Expert-based genotypic interpretation systems are standard methods for guiding treatment selection for patients infected with human immunodeficiency virus type 1. We previously introduced the software pipeline geno2pheno-THEO (g2p-THEO), which on the basis of viral sequence predicts the response to treatment with a combination of antiretroviral compounds by applying methods from statistical learning and the estimated potential of the virus to escape from drug pressure. METHODS We retrospectively validated the statistical model used by g2p-THEO in approximately 7600 independent treatment-sequence pairs extracted from the EuResist integrated database, ranging from 1990 to 2007. Results were compared with the 3 most widely used expert-based interpretation systems: Stanford HIVdb, ANRS, and Rega. RESULTS The difference in receiver operating characteristic curves between g2p-THEO and expert-based approaches was significant (P < .001; paired Wilcoxon test). Indeed, at 80% specificity, g2p-THEO found 16.2%-19.8% more successful regimens than did the expert-based approaches. The increased performance of g2p-THEO was confirmed in a 2001-2007 data set from which most obsolete therapies had been removed. CONCLUSION Finding drug combinations that increase the chances of therapeutic success is the main reason for using decision support systems. The present analysis of a large data set derived from clinical practice demonstrates that g2p-THEO solves this task significantly better than state-of-the-art expert-based systems. The tool is available at http://www.geno2pheno. org.
Phenotypic and Functional Properties of Dendritic Cells Isolated from Human Peripheral Blood in Comparison with Mononuclear Cells and T Cells

Dendritic cells (DCs) are pivotal for antigen presentation, T‐cell priming and B‐cell functions. Few studies have been carried out on DCs in human diseases, partly because the current procedures used for DC preparation include elaborate negative selection with monoclonal antibodies (MoAb) and prolonged culture in cytokine‐enriched milieu, which may influence DC functions. Using physical density and their adherent properties, DCs were prepared from the blood of healthy subjects. Approximately 2% of human blood mononuclear cells (MNC) were shown to consist of DCs, yielding DCs of 80–90% purity. They expressed markers related to DCs (CD1a, CD11c, CD32 and CD83), costimulatory molecules (CD40, CD80, CD86), human leucocyte antigen (HLA) class I and II molecules and inducible nitric oxide (NO) synthase (NOS2), and lacked lymphocyte and monocyte markers (CD3, CD19, CD20, CD56 and CD14). Compared with blood MNC and T cells, DCs showed a high level of spontaneous proliferation and nitric oxide production, as well as strong proliferative responses in mixed leucocyte reactions. Enzyme‐linked immunospot (ELISPOT) assays revealed higher levels of interleukin (IL)‐4‐, IL‐10‐ and interferon‐γ (IFN‐γ)‐secreting cells among DCs than among MNC or T cells obtained from the same blood specimens, while levels of tumour necrosis factor‐α (TNF‐α)‐ and IL‐6‐secreting cells did not differ. The results demonstrate that the method used is fast, effective and competitively priced, and should be useful for studies of DCs in disease states.
Spores as Infectious Propagules of Cryptococcus neoformans

ABSTRACT Cryptococcus neoformans and Cryptococcus gattii are closely related pathogenic fungi that cause pneumonia and meningitis in both immunocompromised and immunocompetent hosts and are a significant global infectious disease risk. Both species are found in the environment and are acquired via inhalation, leading to an initial pulmonary infection. The infectious propagule is unknown but is hypothesized to be small desiccated yeast cells or spores produced by sexual reproduction (opposite- or same-sex mating). Here we characterize the morphology, germination properties, and virulence of spores. A comparative morphological analysis of hyphae and spores produced by opposite-sex mating, same-sex mating, and self-fertile diploid strains was conducted by scanning electron microscopy, yielding insight into hyphal/basidial morphology and spore size, structure, and surface properties. Spores isolated by microdissection were found to readily germinate even on water agarose medium. Thus, nutritional signals do not appear to be required to stimulate spore germination, and as-yet-unknown environmental factors may normally constrain germination in nature. As few as 500 CFU of a spore-enriched infectious inoculum (∼95% spores) of serotype A C. neoformans var. grubii were fully virulent (100% lethal infection) in both a murine inhalation virulence model and the invertebrate model host Galleria mellonella. In contrast to a previous report on C. neoformans var. neoformans, spores of C. neoformans var. grubii were not more infectious than yeast cells. Molecular analysis of isolates recovered from tissues of infected mice (lung, spleen, and brain) provides evidence for infection and dissemination by recombinant spore products. These studies provide a detailed morphological and physiological analysis of the spore and document that spores can serve as infectious propagules.
Why pair? Evidence of aggregative mating in a socially monogamous marine fish (Siganus doliatus, Siganidae)

Many species live in stable pairs, usually to breed and raise offspring together, but this cannot be assumed. Establishing whether pairing is based on mating, or an alternative cooperative advantage, can be difficult, especially where species show no obvious sexual dimorphism and where the act of reproduction itself is difficult to observe. In the tropical marine fishes known as rabbitfish (Siganidae), half of extant species live in socially monogamous, territorial pairs. It has been assumed that partnerships are for mating, but the reproductive mode of pairing rabbitfish is currently unconfirmed. Using passive acoustic telemetry to track movements of fishes belonging to one such species (Siganus doliatus), we provide the first evidence that paired adult fish undertake highly synchronized migrations with multiple conspecifics on a monthly cycle. All tagged individuals migrated along the same route in three consecutive months and were absent from home territories for 2–3 days just after the new moon. The timing and directionality of migrations suggest that S. doliatus may form spawning aggregations, offering the potential for exposure to multiple reproductive partners. The finding raises fundamental questions about the basis of pairing, mate choice and partnership longevity in this family.
Method Development and Validation of Almotriptan in Human Plasma by HPLC Tandem Mass Spectrometry: Application to Pharmacokinetic Study

A simple, sensitive and selective method has been developed for quantification of Almotriptan (AL) in human plasma using Almotriptan-d6 (ALD6) as an internal standard. Almotriptan and Almotriptan-d6 were detected with proton adducts at m/z 336.1→201.1 and 342.2→207.2 in multiple reaction monitoring (MRM) positive mode, respectively. The method was linear over a concentration range of 0.5–150.0 ng/mL. The limit of detection (LOD) and limit of quantification (LOQ) for Almotriptan were 0.2 pg/mL and 0.5 ng/mL, respectively. Liquid-liquid extraction was used followed by MS/MS (ion spray). The method was shown to be precise with an average within-run and between-run variation of 0.68 to 2.78% and 0.57 to 0.86%, respectively. The average within-run and between-run accuracy of the method throughout its linear range was 98.94 to 102.64% and 99.43 to 101.44%, respectively. The mean recovery of drug and internal standard from human plasma was 92.12 ± 4.32% and 89.62 ± 6.32%. It can be applied for clinical and pharmacokinetic studies.
Perinatal Cocaine Exposure Impairs Myocardial &bgr;-Adrenoceptor Signaling in the Neonatal Rat

Cardiac dysfunction occurs in infants with prenatal cocaine exposure, and gestational cocaine exposure induces presynaptic and postsynaptic changes in the central monoaminergic receptor pathways. The hypothesis of this study is that prenatal cocaine exposure adversely affects the peripheral adrenergic receptor (&bgr;AR) signaling pathway in the neonatal rat heart. Timed pregnant rats received daily intragastric treatment with saline or cocaine 20 mg/kg or 60 mg/kg from Gestational Day 2 until parturition. After birth, nursing mothers either continued to receive the same treatment or received no treatment. Adenylyl cyclase activity, &bgr;AR density, and the amount of immunoreactive G proteins were measured in myocardial membranes obtained from the offspring on Postnatal Day 1 or 7. On Postnatal Day 1, prenatal cocaine exposure increased the &bgr;AR number but did not affect isoproterenol-stimulated adenylyl cyclase activity. On Postnatal Day 7, perinatal cocaine exposure significantly attenuated isoproterenol-stimulated adenylyl cyclase activity in the absence of &bgr;AR up-regulation. Prenatal cocaine exposure also significantly increased Gi protein and reduced GTP-stimulated adenylyl cyclase activity in Postnatal Day 1 cocaine (20 mg/kg) pups compared with saline (P < 0.05). Therefore, perinatal cocaine exposure impaired the myocardial &bgr;AR-cAMP signaling pathway during the first week of postnatal life in the rat. Implications This study shows that maternal cocaine use during pregnancy impairs the &bgr;-adrenoceptor signaling pathway in the rat during the first week of life. Abnormal cardiac function in the cocaine-exposed neonate may be related to a defect in &bgr;-adrenoceptors, because they regulate cardiac function.
Composition and Expression of Genes Encoding Carbohydrate-Active Enzymes in the Straw-Degrading Mushroom Volvariella volvacea

Volvariella volvacea is one of a few commercial cultivated mushrooms mainly using straw as carbon source. In this study, the genome of V. volcacea was sequenced and assembled. A total of 285 genes encoding carbohydrate-active enzymes (CAZymes) in V. volvacea were identified and annotated. Among 15 fungi with sequenced genomes, V. volvacea ranks seventh in the number of genes encoding CAZymes. In addition, the composition of glycoside hydrolases in V. volcacea is dramatically different from other basidiomycetes: it is particularly rich in members of the glycoside hydrolase families GH10 (hemicellulose degradation) and GH43 (hemicellulose and pectin degradation), and the lyase families PL1, PL3 and PL4 (pectin degradation) but lacks families GH5b, GH11, GH26, GH62, GH93, GH115, GH105, GH9, GH53, GH32, GH74 and CE12. Analysis of genome-wide gene expression profiles of 3 strains using 3′-tag digital gene expression (DGE) reveals that 239 CAZyme genes were expressed even in potato destrose broth medium. Our data also showed that the formation of a heterokaryotic strain could dramatically increase the expression of a number of genes which were poorly expressed in its parental homokaryotic strains.