Miracle-dz/UniFAR-FTUs huggingface dataset:
A Brief Prehistory of Time

In this thesis we develop an approach to using obsidian hydration date (OHD) chronometric data as a chronology building tool. A Bayesian interpretive framework is developed that enables archaeological chronology to be outlined through OHD data. This is implemented both for OHD as a stand-alone dating system, and for OHD in combination with convention radiocarbon age (CRA) chronometric measurements. On the basis of this development we assess the current utility of OHD as a chronology building tool, and evaluate its future potential. The purpose of this research is two-fold. At a general level the research presented here illustrates how the Bayesian calibration frameworks that have been extensively developed over the past decade (e.g., Naylor and Smith 1988; Buck and Litton 1995; Buck et al. 1991, 1992, 1994a, 1994b, 1994c, 1996; Christen 1994a, 1994b; Christen and Buck 1998; Christen and Litton 1995; Christen et al. 1995; Litton and Buck 1995, 1996; Litton and Leese 1991; Nicholls and Jones 1998, in press; Zeidler et al.1998) can be extended to incorporate other types of chronometric data — OHD in this case. To-date the implementation of Bayesian calibration frameworks have principally focussed on combining CRA data with non-metric temporal data such as the relative ordering of events implied by super-position. However, while radiocarbon is the most widely used chronometric technique in the world other types of chronometric data are more suited to addressing particular tem-
18FDG PET/CT in Routine Surveillance of Asymptomatic Patients following Treatment of Sinonasal Neoplasms

Objective Sinonasal neoplasms have a high rate of recurrence following treatment, and current guidelines support the use of a variety of surveillance techniques. Recent work demonstrates that performance parameters of surveillance modalities may differ with sinonasal tumors in particular when compared with head and neck tumors overall. This study aims to characterize the value of 18fluorodeoxyglucose (18FDG) positron emission tomography/computed tomography (PET/CT) as a screening tool in asymptomatic patients. Study Design Retrospective cohort study. Setting Hospital of the University of Pennsylvania and Pennsylvania hospital. Methods Records of asymptomatic patients without suspicious endoscopy or suspicious imaging other than PET during the first 3 years following definitive treatment for sinonasal malignancy were screened and analyzed for inclusion in the cohort. Disease recurrence was determined by biopsy following suspicious PET evaluation. Results PET/CT scans (n = 111) were performed for 45 disease-free asymptomatic patients with no evidence of disease on endoscopy, and 6.3% were suspicious and prompted biopsy during this period, revealing 3 cases of disease recurrence. Overall specificity for PET/CT alone was 96.3% (95% CI, 90.7%-99.0%), with a negative predictive value of 99% (95% CI, 94.8%-100%). All recurrences were detected between 7 and 12 months, and all patients with true recurrence diagnosed by PET/CT had extrasinonasal involvement of tumor at the time of surgery. Conclusion We examined performance parameters of 18FDG PET/CT in asymptomatic patients with no evidence of disease on endoscopy during the posttreatment period for sinonasal malignancy. The ability of PET/CT to detect recurrences that may be missed by structural imaging or endoscopy makes it a valuable tool for clinicians.
MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures

MOTIVATION Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Taxonomic analysis of microbial communities, a process referred to as binning, is one of the most challenging tasks when analyzing metagenomic reads data. The major problems are the lack of taxonomically related genomes in existing reference databases, the uneven abundance ratio of species and the limitations due to short read lengths and sequencing errors. RESULTS MetaProb is a novel assembly-assisted tool for unsupervised metagenomic binning. The novelty of MetaProb derives from solving a few important problems: how to divide reads into groups of independent reads, so that k-mer frequencies are not overestimated; how to convert k-mer counts into probabilistic sequence signatures, that will correct for variable distribution of k-mers, and for unbalanced groups of reads, in order to produce better estimates of the underlying genome statistic; how to estimate the number of species in a dataset. We show that MetaProb is more accurate and efficient than other state-of-the-art tools in binning both short reads datasets (F-measure 0.87) and long reads datasets (F-measure 0.97) for various abundance ratios. Also, the estimation of the number of species is more accurate than MetaCluster. On a real human stool dataset MetaProb identifies the most predominant species, in line with previous human gut studies. AVAILABILITY AND IMPLEMENTATION https://bitbucket.org/samu661/metaprob CONTACTS cinzia.pizzi@dei.unipd. it or comin@dei.unipd. it SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Redundant Nerve Roots in Patients with Degenerative Lumbar Spinal Stenosis

Extensive fundamental and clinical investigations have been performed concerning redundant nerve roots (RNR) and the pathogenesis of cauda equina claudication (CEC) in degenerative lumbar canal stenosis (DLCS). These investigations consisted of (1) anatomic observations on RNR in 117 fixed cadaveric specimens, (2) myelographic study in 117 patients with or without DLCS, (3) operative observation on neural elements with special reference to the cauda equina in 56 DLCS patients (including a postoperative follow-up), and (4) electrophysiologic tests using spinal cord action potential recording under walking load preoperatively and intraoperative measurement of nerve conduction velocity of RNR. The RNR have neuronal losses resulting from a longer duration stenosis that suggests a sort of friction neuritis. Complicated factors contribute to the pathogenesis of CEC and the development of root gripping, such as the magnitude of RNR, the extent of the stenosis, a narrowed sac, age-dependent axial shortening of the spinal canal, and dynamic or postural factors. In cases with severe RNR, satisfactory operative results can be obtained only after thorough decompression with dural incision.
MIV-310 reduces HIV viral load in patients failing multiple antiretroviral therapy: results from a 4-week phase II study

Background: Drug resistance is an increasing problem in the treatment of HIV infection. MIV-310 (alovudine), a nucleoside reverse transcriptase inhibitor, potently inhibits the replication of highly mutated strains of HIV in vitro. We examined the efficacy of MIV-310 in highly pretreated patients. Methods: In a phase II pilot study, 15 patients failing a current antiretroviral therapy with at least two thymidine-associated mutations (TAM) were given MIV-310 7.5 mg once daily for 4 weeks, in addition to their ongoing treatment. The primary endpoint was the plasma viral load reduction at week 4. Results: At baseline, the median viral load was 3.93 log10 copies/ml and the median CD4 cell count was 360 cells/mm3. After 4 weeks of MIV-310 administration, the median decrease in viral load was −1.13 log10. Interestingly, the median reduction was only −0.57 log10 in the four patients on stavudine, contrasting with a median reduction of −1.88 log10 in the 11 patients not receiving concomitant stavudine. The viral load fell by a median of −1.60 log10 in patients with two to three TAM (n = 7), and by −1.88 log10 in patients with four or five TAM (n = 8). The viral load rebounded in all patients after MIV-310 cessation. No mutations were found in the reverse transcriptase coding region during MIV-310 treatment. MIV-310 was well tolerated, with no serious adverse events and no treatment withdrawals. Conclusion: MIV-310 7.5 mg/day efficiently reduced the HIV viral load in patients failing a multiple-drug regimen. Further studies with different dosages and longer administration times are urgently needed.
Mini symposium on pathogenesis of endometriosis and treatment of endometriosis-associated subfertility. Introduction: the endometriosis enigma.

The European Society of Human Reproduction and Embryology(ESHRE) supports the activities of several Special Interest Groups(SIGs) in various areas of reproductive medicine, includingandrology, embryology, reproductive surgery, early pregnancy,psychology and ethics. The SIG on Endometriosis andEndometrium, founded in 1999, is one of the ‘youngest’ESHRE SIGs and is devoted to stimulating scientiﬁc and clinicalstudies on endometriosis and endometrium. From the beginning,one of the major tasks for this SIG has been to organize aPostgraduate Course at the ESHRE Annual Meetings. So far,three courses have taken place (Bologna, 2000 and Lausanne,2001) or are being planned (Vienna, 2002). This minisymposiumon endometriosis contains three papers that were presented at theﬁrst postgraduate course in Bologna, organized by the authors ofthis article and entitled, ‘New developments in the pathogenesisof endometriosis and in the treatment of endometriosis-associatedsubfertility’. The three papers were submitted and accepted afterthe normal peer review process. Since they cover most of thelectures given at the course, they will be brieﬂy introduced anddiscussed.
Modulation of synaptic input by GABAB receptors improves coincidence detection for computation of sound location

• Organisms localise low frequencies using interaural time disparities (ITDs) in which specialized neurones in the medial superior olive (MSO) compute submillisecond differences in arrival time of sounds to each ear, a value that varies systematically with sound location. • These neurones compute sound location over a 1012 fold range in sound intensities, despite large intensity‐dependent changes in input strength. Modulation of synaptic gain has been suggested as a mechanism to maintain accurate ITD processing. • Here we show that activation of GABAB receptors suppresses both the excitatory and inhibitory inputs to the MSO and alters the kinetics of inhibitory synaptic currents. • Using in vitro physiological methods and computational modelling, we show that the modulation by GABAB receptor activation contributes to spatial tuning of MSO neurones. • These results contribute to the understanding of how neurones maintain computational stability under widely varying input conditions.
Prospective Evaluation of Two-Stage Hepatectomy Combined with Selective Portal Vein Embolisation and Systemic Chemotherapy for Patients with Unresectable Bilobar Colorectal Liver Metastases

Background: Liver resection is contraindicated in patients with multiple bilobar colorectal liver metastases because of the small liver remnant. An alternative strategy which may be curative is a two-stage hepatectomy in which the cancer is resected from one lobe and regeneration allowed prior to contralateral lobe resection. Objective: To assess the feasibility, risks, and outcomes in a prospectively applied strategy for two-stage hepatectomy. Methods: Over a 6-year period, 14 of 280 patients undergoing liver resection for colorectal liver metastases (5%) were considered for two-stage hepatectomy. Surgery was combined with chemotherapy in all (n = 14) and portal vein embolisation (PVE) selectively (n = 5). Median follow-up was 43 months. Results: Both stages were completed in 11 of 14 patients (78%). There were no deaths. Post-operative complication rates were 0% (1st hepatectomy) and 27% (2nd hepatectomy). The 5-year survival after the second hepatectomy was 50%. The mean disease-free survival was 25 ± 7.5 months. Conclusion: Two-stage hepatectomy combined with systemic chemotherapy and PVE can produce long-term survival in patients with multiple bilobar colorectal liver metastases.
Anticoagulation in patients with cancer: an overview of reviews.

INTRODUCTION Relative benefits and harms of anticoagulants are required for judgments regarding appropriate anticoagulation in patients with cancer. OBJECTIVES To review the benefits and harms of anticoagulants for prophylactic, therapeutic, and survival improvement indications in patients with cancer. PATIENTS AND METHODS Overview of 6 systematic reviews of anticoagulation in cancer following the Cochrane Collaboration and Grading of Recommendations Assessment, Development and Evaluation methodology. RESULTS Central venous catheters thromboprophylaxis with heparin or warfarin does not significantly reduce the incidence of symptomatic deep vein thrombosis (DVT) (relative risk [RR] 0.43, 95% CI 0.18-1.06 and RR 0.62, 95% CI 0.30-1.27 respectively). For perioperative thromboprophylaxis, low-molecular-weight heparin (LMWH) and unfractionated heparin (UFH) have similar effects on mortality (RR 0.89, 95% CI 0.61-1.28) and morbidity outcomes. For the initial treatment of venous thromboembolism (VTE), LMWH compared with UFH reduces mortality at 3 months (RR 0.71, 95% CI 0.52-0.98). For the long-term treatment of VTE, LMWH compared with vitamin K antagonists reduces VTE recurrence (hazard ratio [HR] 0.47, 95% CI 0.32-0.71) but not mortality (HR 0.96, 95% CI 0.81-1.14). As interventions to improve survival, warfarin suggests a survival benefit at 6 months in the subgroup of small cell lung cancer (SCLC) (RR 0.69, 95% CI 0.50-0.96) while heparin suggests a survival benefit in patients with cancer in general (HR 0.77, 95% CI 0.65-0.91) and in those with limited SCLC in particular (HR 0.56, 95% CI 0.38-0.83). CONCLUSIONS In patients with cancer, current evidence does not support routine use of thromboprophylaxis for central venous catheters or a specific anticoagulant for perioperative thromboprophylaxis. Anticoagulants may improve survival, but more data will be useful in deciding which subgroups benefit most.
Terrorism, Distress, and Drinking: Vulnerability and Protective Factors

Research has demonstrated effects of 9/11 on distress and drinking outcomes in individuals directly affected and indirectly affected across the United States. Fewer studies have addressed vulnerability and protective factors shown to moderate the effects of stress exposure. We report findings from a Midwestern workplace cohort study. Respondents to a 6 wave longitudinal mail survey completed questionnaires prior to September 11, 2001 and again in 2003 and 2005. Regression analyses encompassed measures of terrorism-related beliefs and fears, workplace stressors (sexual harassment, generalized abuse and low decision latitude), marital and parental status, and perceived social support in 2003, and distress and deleterious drinking outcomes in 2005. Analyses showed that terrorism-related fears significantly interacted with workplace stressors and interpersonal social relationships in predicting distress, drinking or both, controlling for pre-9/11 distress and drinking. Gender differences were also found. This article suggests that certain individuals may be at heightened risk for distressful reactions to and/or deleterious drinking resulting from terrorism-related issues and fears due to additional risk factors involving workplace stressors and inadequate interpersonal bonds. However, limitations of the study were noted and future research was recommended.
Modélisation tridimensionnelle du comportement mécanique de la garniture de forage dans les puits à trajectoires complexes : application à la prédiction des frottements garniture-puits

Reussir le forage d'un puits petrolier le plus rapidement possible et a moindre cout est devenu un defi continu pour les professionnels du secteur. Pour relever ce defi, un bon dimensionnement des installations de forage s'impose. La meilleure prediction des pertes liees aux frottements entre la garniture de forage et les parois du puits, notamment pour les puits a trajectoires fortement deviees, est un atout majeur pour ce dimensionnement. Les modeles usuels de prediction des frottements montrent certaines insuffisances lorsque la trajectoire du puits se complexifie. Un nouveau modele de calcul de frottements dans les puits de forage a trajectoires complexes a ete developpe et valide. Ce modele utilise une methode tridimensionnelle de reconstitution de la trajectoire integrant a la fois la courbure et la torsion geometrique. Contrairement aux modeles classiques, qui supposent simplement que la garniture repose par gravite sur la paroi basse du trou de forage et qui negligent souvent la rigidite des tiges, le nouveau modele rigide calcule la vraie deformee de la garniture de forage a l'interieur du trou via un algorithme iteratif de contact unilateral. En outre, pour un gain important du temps de calcul, le modele se base sur une integration numerique directe des equations d'equilibre local sans avoir recours a la methode des elements finis. La comparaison avec un modele couramment utilise dans l'industrie de forage, appele modele LISSE, a ete effectuee sur plusieurs puits reels et theoriques. Il ressort de cette comparaison que le nouveau modele vient palier plusieurs faiblesses du modele LISSE dans le cas des trajectoires a geometrie complexe (surestimation des zones de contacts et des forces de contact en presence de micro-tortuosite, non sensibilite au signe du gradient d'azimut en presence de fort gauchissement, hypothese de contact sur la paroi basse du trou pas toujours verifiee). Par ailleurs, la confrontation avec les mesures du terrain pour la plupart des puits a geometrie bidimensionnelle ou faiblement tridimensionnelle avec des faibles dog legs (ne depassant pas 2 a 3°/30 m) fournit generalement des concordances entre les resultats des deux types de modeles et les valeurs mesurees. En revanche, en presence de tortuosites et dog legs locaux le nouveau modele fournit une meilleure prediction des pertes en frottement.
The fate and effects of xenobiotics in human placenta

During past decades, knowledge on placental drug metabolism and mechanisms of placental transfer has increased significantly. Most pharmaceutical drugs administered during pregnancy cross the placenta to some extent. The important properties determining the placental transfer by passive diffusion are molecular weight, pKa, lipid solubility and protein binding. In addition to passive diffusion, compounds may cross the placenta via active transfer, facilitated diffusion, phagocytosis and pinocytosis. This review gives an update of efflux transporter proteins and xenobiotic-metabolizing enzymes that modify the fate and effects of drugs in the placenta.
Trajectories of care: Spouses coping with changes related to mild cognitive impairment

Mild cognitive impairment (MCI) refers to non-normative changes in memory and cognition. While researchers are beginning to address the social consequences of MCI, no investigations have tracked how married couples respond to MCI over time as symptoms stabilize or become more severe. Guided by life course and symbolic interactionist tenets, we examined how 40 older couples in the United States adjusted to daily life after one partner was diagnosed with MCI and how their marital roles and relationship changed over a three- to four-year period. Data were collected from 2004 through 2010. All couples experienced an initial period of transition in coping with MCI where they made adjustments in their daily lives and interactions. Following this adjustment period, four trajectories of care emerged depending on the extent of the older adult’s decline and the spouse’s response. We conclude that changes associated with MCI affect role identity and have consequences for spousal relationships.
Non-Gaussianity in WMAP data due to the correlation of CMB lensing potential with secondary anisotropies

We measure the skewness power spectrum of the CMB anisotropies optimized for a detection of the secondary bispectrum generated by the correlation of the CMB lensing potential with integrated Sachs-Wolfe effect and the Sunyaev-Zel'dovich effect. The covariance of our measurements is generated by Monte Carlo simulations of Gaussian CMB fields with noise properties consistent with WMAP 5-year data. When interpreting multifrequency measurements we also take into account the confusion resulting from unresolved radio point sources. We analyze Q, V and W-band WMAP 5-year raw and foreground-cleaned maps using the KQ75 mask out to l{sub max}=600. We find no significant evidence for a nonzero non-Gaussian signal from the lensing-secondary correlation in all three bands and we constrain the overall amplitude of the cross-power spectrum between CMB lensing potential and the sum of SZ and ISW fluctuations to be 0.42{+-}0.86 and 1.19{+-}0.86 in combined V and W-band raw and foreground-cleaned maps provided by the WMAP team, respectively. The point-source amplitude at the bispectrum level measured with this skewness power spectrum is higher than previous measurements of point-source non-Gaussianity. We also consider an analysis where we also account for the primordial non-Gaussianity in addition to lensing-secondary bispectrum and point sources. The focus ofmore » this paper is on secondary anisotropies. Consequently the estimator is not optimized for primordial non-Gaussianity and the limit we find on local non-Gaussianity from the foreground-cleaned V+W maps is f{sub NL}=-13{+-}62, when marginalized over point sources and lensing-ISW/SZ contributions to the total bispectrum. « less
Isolation and characterization of Pseudomonas aeruginosa mutants requiring salicylic acid for pyochelin biosynthesis

Pseudomonas aeruginosa mutants requiring salicylic acid for pyochelin biosynthesis were isolated after chemical mutagenesis by plating on a siderophore detection medium. Like the wild type, these mutants incorporated 7-[14C]salicylic acid into pyochelin, demonstrating that salicylic acid is an intermediate in the biosynthesis pathway of pyochelin.
Factors related to genetic testing in adults at risk for Huntington disease: the prospective Huntington at‐risk observational study (PHAROS)

Huntington disease (HD) is a late onset ultimately fatal neurodegenerative disorder caused by a cytosine–adenine–guanine ( CAG) triplet repeat expansion in the Huntingtin gene which was discovered in 1993. The PHAROS study is a unique observational study of 1001 individuals at risk for HD who had not been previously tested for HD and who had no plans to do so. In this cohort, 104 (10%) individuals changed their minds and chose to be tested during the course of the study but outside of the study protocol.
Recurrent inhibition is increased in patients with spinal cord injury

Mechanisms underlying the development of spasticity after spinal cord injury are not understood. One spinal interneuron likely to be affected is the Renshaw cell, which acts to produce recurrent inhibition in motor neurons as well as inhibiting Ia interneurons. Descending pathways exert both excitatory and inhibitory control over Renshaw cell activity. We studied Renshaw cell activity in normal subjects and in patients with varying levels of spasticity after spinal cord injury using the conditioned H-reflex technique of Pierrot-Deseilligny and Bussel. A submaximal stimulus to the tibial nerve is presented prior to a supramaximal stimulus so that action potential collision permits an H reflex (H') to be elicited in response to the supramaximal stimulus. The amplitude of this H' reflex is affected by activity in recurrent inhibitory pathways. Patients with both complete and partial spinal cord lesions were studied; date of injury ranged from 1 month to 216 months prior to evaluation. In the 18 patients in whom H reflexes could be recorded, H' reflexes were absent in 13, in contrast to their uniform presence in normal subjects. We conclude that recurrent inhibition via Renshaw cell activity is increased in spinal cord injury, and that measures of recurrent inhibition may correlate well with some clinical measures of spasticity.