Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of land use and survey design on trip underreporting in Montreal and Toronto’s regional surveys

This paper contributes to the literature on travel survey methods by quantifying the relationship between land use, data collection protocol and trip under-reporting in regional travel surveys. While under-reporting more broadly is a recognized problem, the significant increase in underreporting in denser, more urban-type environments identified here has never before been demonstrated or measured. Consequences of this land use-related bias for transportation planning and modelling are explored. The work is carried out by comparing the results of two very similar household travel surveys conducted in 2011 and 2013, in Toronto and Montreal respectively. Using data on over 350,000 persons, a binary logit model for discretionary trip making is estimated and the effects of land use and data collection protocol on under-reporting are isolated. This is done by controlling for mobility tool access, household type and other key determinants of travel demand. Counterintuitive effects for urban type environments found indicate the under-reporting effect is equivalent to a reduction in the pre-existing odds of reporting discretionary trip making in more urban environments of 19 to 29%. When combined with Toronto’s data collection protocol effect, the range increases to 39 to 55%. Results should be of use to transportation planning authorities wishing to make better use of the data collected in large surveys. Recognizing some of the flaws and biases in what is reported, these authorities can complement existing sources of data or modify their approaches to demandbased infrastructure provision to better account for the large number of, largely pedestrian, unreported trips.
Leptomeningeal metastasis after surgical resection of brain metastases

OBJECTIVE To determine the incidence and risk factors for leptomeningeal metastasis after surgery for brain metastasis of solid tumors. METHODS Review of the records of all patients operated on for brain metastasis between January 1990 and August 1995. RESULTS In this period 28 patients underwent surgery for brain metastasis, of whom 27 were available for evaluation in this study. Median survival after craniotomy was 11 months. Nine patients (33%) developed leptomeningeal metastasis 2–13 months after surgery, which included six of the nine patients operated on for posterior fossa metastasis (p=0.05). In five patients, leptomeningeal metastasis was the only site of recurrence. Three patients developed the leptomeningeal metastasis as bulky tumour along the spinal cord, which is a rare presentation. No other risk factors for the development of leptomeningeal metastasis other than surgery for posterior fossa metastasis were identified. CONCLUSIONS There is an increased risk of leptomeningeal metastasis after surgery for posterior fossa metastasis. Future trials should consider the value of an active approach to this complication in these patients.
Testing of the analytical anisotropic algorithm for photon dose calculation.

The analytical anisotropic algorithm (AAA) was implemented in the Eclipse (Varian Medical Systems) treatment planning system to replace the single pencil beam (SPB) algorithm for the calculation of dose distributions for photon beams. AAA was developed to improve the dose calculation accuracy, especially in heterogeneous media. The total dose deposition is calculated as the superposition of the dose deposited by two photon sources (primary and secondary) and by an electron contamination source. The photon dose is calculated as a three-dimensional convolution of Monte-Carlo precalculated scatter kernels, scaled according to the electron density matrix. For the configuration of AAA, an optimization algorithm determines the parameters characterizing the multiple source model by optimizing the agreement between the calculated and measured depth dose curves and profiles for the basic beam data. We have combined the acceptance tests obtained in three different departments for 6, 15, and 18MV photon beams. The accuracy of AAA was tested for different field sizes (symmetric and asymmetric) for open fields, wedged fields, and static and dynamic multileaf collimation fields. Depth dose behavior at different source-to-phantom distances was investigated. Measurements were performed on homogeneous, water equivalent phantoms, on simple phantoms containing cork inhomogeneities, and on the thorax of an anthropomorphic phantom. Comparisons were made among measurements, AAA, and SPB calculations. The optimization procedure for the configuration of the algorithm was successful in reproducing the basic beam data with an overall accuracy of 3%, 1mm in the build-up region, and 1%, 1mm elsewhere. Testing of the algorithm in more clinical setups showed comparable results for depth dose curves, profiles, and monitor units of symmetric open and wedged beams below dmax. The electron contamination model was found to be suboptimal to model the dose around dmax, especially for physical wedges at smaller source to phantom distances. For the asymmetric field verification, absolute dose difference of up to 4% were observed for the most extreme asymmetries. Compared to the SPB, the penumbra modeling is considerably improved (1%, 1mm). At the interface between solid water and cork, profiles show a better agreement with AAA. Depth dose curves in the cork are substantially better with AAA than with SPB. Improvements are more pronounced for 18MV than for 6MV. Point dose measurements in the thoracic phantom are mostly within 5%. In general, we can conclude that, compared to SPB, AAA improves the accuracy of dose calculations. Particular progress was made with respect to the penumbra and low dose regions. In heterogeneous materials, improvements are substantial and more pronounced for high (18MV) than for low (6MV) energies.
Isolation and characterization of type IV group B Streptococcus capsular polysaccharide

An antigenically distinct serotype, type IV, has recently been added to the recognized serotypes of group B streptococci (GBS). We isolated and purified the capsular polysaccharide antigen from a prototype type IV GBS strain. The type IV capsular polysaccharide formed a precipitin line with rabbit antiserum to type IV GBS organisms but not with antiserum to organisms of GBS serotype Ia, Ib, II, or III. Enzyme-linked immunosorbent assay inhibition experiments showed no cross-reaction between type IV antiserum and other GBS serotypes. Capsular polysaccharide released from the bacterial cells with mutanolysin and that isolated from the culture supernatant had similar elution profiles on Sepharose CL-6B, with a Kav of 0.30 and an estimated Mr of 200,000. The purified type IV polysaccharide was found to contain galactose, glucose, N-acetylglucosamine, and N-acetylneuraminic acid (sialic acid) as exclusive sugars. The polysaccharide contained 23% (by weight) sialic acid and galactose, glucose, and N-acetylglucosamine in a relative ratio of (1):1.10:0.55. These results are compatible with a repeating structure of six monosaccharide residues containing galactose, glucose, N-acetylglucosamine, and sialic acid in a molar ratio of 2:2:1:1. Unlike type Ia, II, and III GBS polysaccharides, desialylation of the type IV polysaccharide produced an antigen which formed a line of identity with the native type IV antigen in double diffusion in agar against homologous antiserum. This result suggests that sialic acid is not as critical to the immunodeterminant structure of the type IV antigen as it is for other GBS capsular types.
Comparison of Initial Experiences of Robot-Assisted Radical Cystectomy with those of Laparoscopic for Bladder Cancer

Objective The aim of the present study was to evaluate perioperative outcomes in initial experiences of robot-assisted laparoscopic radical cystectomy (RARC) in comparison with those of laparoscopic radical cystectomy (LRC) for muscle-invasive or high-risk non-muscle-invasive bladder cancer. Methods We performed RARC on six patients with muscle-invasive or high-risk non-muscle-invasive bladder cancer starting in October 2011. During the same period, another five patients underwent LRC. Perioperative outcomes in initial experiences of RARC were elucidated by comparing them with those of LRC. Results Robot-assisted procedures were completed in all cases without conversion to open surgery. The median time of pneumoperitoneum was 252 minutes, and the median blood loss was 340 mL. No severe complications were observed. Perioperative outcomes did not significantly differ between RARC and LRC. Although two cases of troubles in uretero-conduit anastomosis sites were observed after LRC, no patients experienced postoperative complication related to urinary diversion after RARC. Conclusions Our data indicate that RARC is an acceptable option even in the initial period, and it may become one of the most favorable procedures for treatment of muscle-invasive bladder cancer in the near future, although more tests and longer follow-ups are required to confirm its effectiveness and safety.
Pregnancy-Associated Breast Cancer: Clinicopathological Characteristics of 20 Cases with a Focus on Identifiable Causes of Diagnostic Delay

Background: The primary objective of this study was to evaluate the clinicopathological characteristics of patients with pregnancy-associated breast cancer (PABC), with a special focus on diagnostic delays and the identifiable causes of diagnostic delays. Patients and methods: Clinicopathological data of patients treated for PABC between 2003 and 2012 at Hacettepe University Hospital was retrospectively reviewed. Results: 20 patients with PABC were included. The pathological examination revealed predominance of invasive ductal carcinoma (80%), grade III tumors (65%) and advanced-stage (III-IV) disease (75%). In 8 patients (40%), there was a diagnostic delay between occurrence of the presenting symptoms and the initiation of breast mass workup. For these 8 patients, the main identifiable causes of diagnostic delay were the attribution of disease-related symptoms to pregnancy or lactation in 5 (63%) and negligence of symptoms in 2 (25%). Conclusions: PABC mostly presents with advanced-stage disease, and there can be a substantial diagnostic delay before these patients receive treatment. Preconceptional, gestational and postpartum examination of women of reproductive age should include a thorough breast examination and should provide adequate information regarding the physiological changes in breast tissue and the possible pathological symptoms.
The growth of knowledge through the resource-based view

The resource-based view (RBV) has not previously been conceptualized as a theoretical framework encompassing metaphysical and empirical perspectives. The purpose of this paper is to logically analyze the evolutionary process of the RBV, triggered by “rigidity. ” It attempts to clarify the significance and limitations of the RBV. ,Based on Popper’s methodological model of the growth of knowledge, the study analyzed and evaluated the evolution of the RBV. ,The RBV has evolved in three phases. The sub-problems have changed through empirical testing on the basis of one metaphysical problem and one metaphysical theory. Thus, the evolution may indicate progress within one framework. However, during phase 3, the ambiguity of concept may inhibit the growth of knowledge. For further progress, it is necessary to overcome the vulnerability of the RBV’s metaphysical statements. ,This paper shows the possibility of the growth of knowledge within the RBV framework and for a new framework to emerge due to its limitations. It should contribute both theoretically and practically to the field of strategic management. ,Popper’s model was used to examine a previously neglected topic, namely, the growth of knowledge in the evolution of the RBV. Moreover, considering “rigidity” as corresponding to a process of error elimination is a novel approach, clearly revealing the dynamism of the RBV’s evolution.
Isokinetic strength characteristics of the quadriceps femoris and hamstring muscles in high school students.

The purpose of this study was to determine the isokinetic strength of the quadriceps femoris and hamstring muscles in high school-aged students. Forty-seven 15- to 18-year-old high school volunteers served as subjects. Data were gathered on each subject by a questionnaire, lower extremity musculoskeletal assessment, and isokinetic testing of the two muscle groups at 60 degrees/sec and 180 degrees/sec. This study found no age effect on peak torque and no significant differences in peak torque between dominant and nondominant limbs. Significant differences (p less than .001) occurred between the isokinetic strength of male and female subjects. The average hamstring muscle to quadriceps femoris muscle torque ratio was 57 percent at 60 degrees/sec and 70 percent at 180 degrees/sec. A value of foot pounds of torque per kilogram of body weight was provided as a guideline for clinicians. This investigation supports several findings already reported for other age groups.
CRISPR/Cas9 knockout of USP18 enhances type I IFN responsiveness and restricts HIV‐1 infection in macrophages

The IFN‐stimulated gene ubiquitin‐specific proteinase 18 (USP18) encodes a protein that negatively regulates T1 IFN signaling via stearic inhibition of JAK1 recruitment to the IFN‐α receptor 2 subunit (IFNAR2). Here, we demonstrate that USP18 expression is induced by HIV‐1 in a T1 IFN‐dependent manner. Experimental depletion of USP18 by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9) gene editing results in a significant restriction of HIV‐1 replication in an induced pluripotent stem cell (iPSC)‐derived macrophage model. In the absence of USP18, macrophages have increased responsiveness to stimulation with T1 IFNs with prolonged phosphorylation of STAT1 and STAT2 and increased expression of IFN‐stimulated genes that are key for antiviral responses. Interestingly, HIV‐1 requires some signaling through the T1 IFN receptor to replicate efficiently because a neutralizing antibody that inhibits T1 IFN activity reduces HIV‐1 replication rate in monocyte‐derived macrophages. USP18 induction by HIV‐1 tunes the IFN response to optimal levels allowing for efficient transcription from the HIV‐1 LTR promoter while minimizing the T1 IFN‐induced antiviral response that would otherwise restrict viral replication and spread. Finally, iPSC and CRISPR/Cas9 gene targeting offer a powerful tool to study host factors that regulate innate immune responses.
Lactate elicits vascular endothelial growth factor from macrophages: a possible alternative to hypoxia

Macrophages respond to various stimuli to produce angiogenic factors but few mechanistic details are known. We examined the effects of hypoxia, lactate and nicotinamide on the expression of vascular endothelial growth factor by cultured macrophages. These agents were chosen because they down‐regulate polyadenosine diphosphoribose levels. Following exposure, conditioned media were analyzed for vascular endothelial growth factor protein. Nicotinamide adenine dinucleotide, polyadenosine diphosphoribose, and vascular endothelial growth factor mRNA were measured in the cellular fraction. Angiogenic capacity of the conditioned media was tested in rabbit corneas and Matrigel implants.
Heritabilities and correlations among body condition scores, production traits, and reproductive performance.

The objectives of this study were to estimate the heritability of body condition scores (BCS) from producer and consultant-recorded data and to describe the genetic and phenotypic relationships among BCS, production traits, and reproductive performance. Body condition scores were available at calving, postpartum, first service, pregnancy check, before dry off, and at dry off from the Dairy Records Management Systems in Raleigh, NC, through the PCDART program. Heritabilities, genetic correlations, and phenotypic correlations were estimated assuming an animal model using average information REML. Herd-year-season effects and age at calving were included in all models. Prior calving interval was included in models for second and third lactations. Analyses that included reproductive traits were conducted with and without mature equivalent milk as a covariable. Heritability estimates for BCS ranged from 0.09 at dry-off to 0.15 at postpartum in first lactation. Heritability estimates ranged from 0.07 before dry-off to 0.20 at pregnancy check in second lactation and from 0.08 before dry-off to 0.19 at first service in third lactation. Genetic correlations between adjacent BCS within first lactation were greater than 0.96 with the exception of calving and postpartum (0.74). In second lactation, adjacent genetic correlations were 1.0 with the exception of calving and postpartum (0.84). Genetic correlations across lactations were greater than 0.77. Phenotypic correlations between scoring periods were highest for adjacent scoring periods and when BCS was lowest. Phenotypic correlations were lower than genetic correlations, i.e., less than 0.70. Higher BCS during the lactation were negatively related to production, both genetically and phenotypically, but the relationship was moderate. Higher BCS were favorably related genetically to reproductive performance during the lactation.
Long-term results after endoscopic pancreatic stent placement without pancreatic papillotomy in acute recurrent pancreatitis due to pancreas divisum.

BACKGROUND There is no consensus regarding the appropriate endoscopic treatment for acute recurrent pancreatitis associated with pancreas divisum. Endoscopic papillotomy of the minor papilla appears to yield improvement in most cases, but optimal depth and height have not been defined. METHODS Endoscopic pancreatic stent placement after minor papilla dilation was performed in 25 patients with pancreas divisum and acute recurrent pancreatitis. Five patients drank alcohol daily; no other cause of pancreatitis was detected. After adequate dilation, a transpapillary pancreatic stent (5F to 7F, 5 to 7 cm) was inserted over a guidewire into the dorsal duct. The stent was replaced twice, after 2- to 3-month intervals. RESULTS While stents were in place, no further episodes of pancreatitis occurred in 23 patients. However, dorsal duct changes of unknown clinical significance were seen in 21 cases. At mean follow-up of 24 months (range 3 to 70 months) after stent removal, 19 (76%) remained symptom free. Pancreatitis recurred in 6 patients during the follow-up after final stent removal; no further pancreatitis occurred in 2 of 3 who underwent repeat stent insertion. Complications in the series were minimal. CONCLUSION Endoscopic pancreatic stent placement after minor papilla and dorsal duct dilation, without endoscopic papillotomy, provided safe and effective endoscopic treatment in patients with pancreas divisum and acute recurrent pancreatitis.
Mechanism for Active Membrane Fusion Triggering by Morbillivirus Attachment Protein

ABSTRACT The paramyxovirus entry machinery consists of two glycoproteins that tightly cooperate to achieve membrane fusion for cell entry: the tetrameric attachment protein (HN, H, or G, depending on the paramyxovirus genus) and the trimeric fusion protein (F). Here, we explore whether receptor-induced conformational changes within morbillivirus H proteins promote membrane fusion by a mechanism requiring the active destabilization of prefusion F or by the dissociation of prefusion F from intracellularly preformed glycoprotein complexes. To properly probe F conformations, we identified anti-F monoclonal antibodies (MAbs) that recognize conformation-dependent epitopes. Through heat treatment as a surrogate for H-mediated F triggering, we demonstrate with these MAbs that the morbillivirus F trimer contains a sufficiently high inherent activation energy barrier to maintain the metastable prefusion state even in the absence of H. This notion was further validated by exploring the conformational states of destabilized F mutants and stabilized soluble F variants combined with the use of a membrane fusion inhibitor (3g). Taken together, our findings reveal that the morbillivirus H protein must lower the activation energy barrier of metastable prefusion F for fusion triggering.
Simple and robust methods for support vector expansions

Most support vector (SV) methods proposed in the recent literature can be viewed in a unified framework with great flexibility in terms of the choice of the kernel functions and their constraints. We show that all these problems can be solved within a unique approach if we are equipped with a robust method for finding a sparse solution of a linear system. Moreover, for such a purpose, we propose an iterative algorithm that can be simply implemented. Finally, we compare the classical SV approach with other, recently proposed, cross-correlation based, alternative methods. The simplicity of their implementation and the possibility of exactly calculating their computational complexity constitute important advantages in a real-time signal processing scenario.
Eating patterns and risk of colon cancer.

Colon cancer has been associated with several nutrients and foods. The authors used data from a population-based study conducted in Northern California, Utah, and Minnesota to examine associations between dietary eating patterns and risk of developing colon cancer. Through factor analysis, detailed dietary intake data obtained from 1,993 cases (diagnosed in 1991-1994) and 2,410 controls were grouped into factors that were evaluated for relations with lifestyle characteristics and colon cancer risk. Several dietary patterns emerged. The dietary patterns with the most variation were labeled "Western," "prudent," "high fat/sugar dairy," "substituters," and "drinkers. " The "Western" dietary pattern was associated with a higher body mass index and a greater intake of total energy and dietary cholesterol. The "prudent" pattern was associated with higher levels of vigorous leisure time physical activity, smaller body size, and higher intakes of dietary fiber and folate. Persons who had high scores on the "drinker" pattern were also more likely to smoke cigarettes. The "Western" dietary pattern was associated with an increased risk of colon cancer in both men and women. The association was strongest among people diagnosed prior to age 67 years (for men, odds ratio (OR)=1.96, 95% confidence interval (CI) 1.22-3.15; for women, OR=2.02, 95% CI 1.21-3.36) and among men with distal tumors (OR=2.25, 95% CI 1.47-3.46). The "prudent" diet was protective, with the strongest associations being observed among people diagnosed prior to age 67 years (men: OR=0.63, 95% CI 0.43-0.92; women: OR=0.58, 95% CI 0.38-0.87); associations with this dietary pattern were also strong among persons with proximal tumors (men: OR=0.55, 95% CI 0.38-0.80; women: OR=0.64, 95% CI 0.45-0.92). Although "substituters" (people who substituted low fat dairy products for high fat dairy products, margarine for butter, poultry for red meat, and whole grains for refined grains) were at reduced risk of colon cancer, the reduction in risk was not statistically significant. These data support the hypothesis that overall dietary intake pattern is associated with colon cancer, and that the dietary pattern associated with the greatest increase in risk is the one which typifies a Western-style diet.
MR cholangiography in orthotopic liver transplantation: sensitivity and specificity in detecting biliary complications

Boraschi P, Donati F, Gigoni R, Volpi A, Salemi S, Filipponi F, Falaschi F. MR cholangiography in orthotopic liver transplantation: sensitivity and specificity in detecting biliary complications. Clin Transplant 2010: 24: E82–E87. © 2009 John Wiley & Sons A/S.