LLukas22/scidocs huggingface dataset:
New advances in DPYD genotype and risk of severe toxicity under capecitabine

BACKGROUND
Deficiency in dihydropyrimidine dehydrogenase (DPD) enzyme is the main cause of severe and lethal fluoropyrimidine-related toxicity. Various approaches have been developed for DPD-deficiency screening, including DPYD genotyping and phenotyping. The goal of this prospective observational study was to perform exhaustive exome DPYD sequencing and to examine relationships between DPYD variants and toxicity in advanced breast cancer patients receiving capecitabine.


METHODS
Two-hundred forty-three patients were analysed (88.5% capecitabine monotherapy). Grade 3 and grade 4 capecitabine-related digestive and/or neurologic and/or hemato-toxicities were observed in 10.3% and 2.1% of patients, respectively. DPYD exome, along with flanking intronic regions 3'UTR and 5'UTR, were sequenced on MiSeq Illumina. DPD phenotype was assessed by pre-treatment plasma uracil (U) and dihydrouracil (UH2) measurement.


RESULTS
Among the 48 SNPs identified, 19 were located in coding regions, including 3 novel variations, each observed in a single patient (among which, F100L and A26T, both pathogenic in silico). Combined analysis of deleterious variants *2A, I560S (*13) and D949V showed significant association with grade 3-4 toxicity (sensitivity 16.7%, positive predictive value (PPV) 71.4%, relative risk (RR) 6.7, p<0.001) but not with grade 4 toxicity. Considering additional deleterious coding variants D342G, S492L, R592W and F100L increased the sensitivity to 26.7% for grade 3-4 toxicity (PPV 72.7%, RR 7.6, p<0.001), and was significantly associated with grade 4 toxicity (sensitivity 60%, PPV 27.3%, RR 31.4, p = 0.001), suggesting the clinical relevance of extended targeted DPYD genotyping. As compared to extended genotype, combining genotyping (7 variants) and phenotyping (U>16 ng/ml) did not substantially increase the sensitivity, while impairing PPV and RR.


CONCLUSIONS
Exploring an extended set of deleterious DPYD variants improves the performance of DPYD genotyping for predicting both grade 3-4 and grade 4 toxicities (digestive and/or neurologic and/or hematotoxicities) related to capecitabine, as compared to conventional genotyping restricted to consensual variants *2A, *13 and D949V.
Effects of the Use of Smartphones on Pain and Muscle Fatigue in the Upper Extremity

[Purpose] The purpose of this study was to investigate the effect of the use of smartphones on the upper extremity and determine whether there were differences in these changes between smartphone and computer use. [Subject] Forty healthy young adults (18 male, 25 female) took part in this study. [Methods] The pressure pain threshold measurement was assessed at the center of the upper trapezius of the dominant upper limb of the subjects. Electrodes were attached to the subjects in the two experiment groups, who then continuously performed a typing task on their own personal smartphone or computer keyboard for ten minutes. [Results] Regarding the pressure pain threshold of the upper trapezius, the smartphone and computer use groups showed significant decreases after performing the task compared with before it. Regarding muscle fatigue in the four monitored muscles, the smartphone and computer use groups showed deceases in median frequencies in all muscles measured after performing the tasks. The smartphone use group showed statistically significant differences in the brachioradialis, and the computer use group showed statistically significant differences in the upper trapezius when compared with the control group (p <0.05). [Conclusion] We found feasible relationships between smartphone use and musculoskeletal symptoms of the upper extremity and neck and identified physical differences between the smartphone use and computer use.
LayoutNet: Reconstructing the 3D Room Layout from a Single RGB Image

We propose an algorithm to predict room layout from a single image that generalizes across panoramas and perspective images, cuboid layouts and more general layouts (e.g. "L"-shape room). Our method operates directly on the panoramic image, rather than decomposing into perspective images as do recent works. Our network architecture is similar to that of RoomNet [15], but we show improvements due to aligning the image based on vanishing points, predicting multiple layout elements (corners, boundaries, size and translation), and fitting a constrained Manhattan layout to the resulting predictions. Our method compares well in speed and accuracy to other existing work on panoramas, achieves among the best accuracy for perspective images, and can handle both cuboid-shaped and more general Manhattan layouts.
The Historical Geography Imperative

Abstract The fortieth anniversary of Ralph Brown's Historical Geography of the United States provides an appropriate occasion to review some of the accomplishments and status of North American historical geography. This small but expanding field has produced a very substantial literature, including several new landmark publications during the past year. Historical geographers have earned high respect in the large world of historical scholarship and are participating in the general reassessment of national histories. They have also been successfully reaching out to a broader public. However, despite such accomplishments and recognition outside geography, historical geography is seriously underrepresented in academic departments. Overcoming that incongruity is one of the obvious and essential ways of strengthening the dangerously weak field of American geography in general.
Cocoa in Ghana : Shaping the Success of an Economy

o other country comes to mind more than Ghana when one speaks of cocoa. Likewise, one cannot think of Ghana without thinking of its cocoa sector, which offers livelihoods for over 700,000 farmers in the southern tropical belt of the country. Long one of Ghana’s main exports, cocoa has been central to the country’s debates on development, reforms, and poverty alleviation strategies since independence in 1957. The cocoa sector in Ghana has not been an unmitigated success, however. After emerging as one of the world’s leading producers of cocoa, Ghana experienced a major decline in production in the 1960s and 1970s, and the sector nearly collapsed in the early 1980s. Production steadily recovered in the mid-1980s after the introduction of economywide reforms, and the 1990s marked the beginning of a revival, with production nearly doubling between 2001 and 2003. These ups and downs offer interesting lessons. Various administrations in Ghana, including the colonial one, have used cocoa as a source of public revenue, and in so doing the Ghanaian experience offers a recurrent example of a policy practice followed by many other African countries: taxing the country’s major export sector to finance public expenditure (Herbst 1993). Revenue extraction by the state has had varying effects on production depending on global prices, marketing costs, explicit taxes on the sector, and macroeconomic conditions such as inflation and overvaluation of exchange rates and inelasticity of cocoa supplies. Regardless of the level of extraction, the need for sound macroeconomic management, of inflation and exchange rates in particular, becomes evident for continuing to offer incentives for production. The other is the need for Ghana’s cocoa pricing policy to arrive at a marketing arrangement that does not kill the goose that lays the golden eggs. Ghana appears to have achieved such as arrangement without fully liberalizing the sector as other producers in West Africa have.
Service quality , customer satisfaction , and customer value : A holistic perspective

The author proposes and tests an integrative model of service quality, customer value, and customer satisfaction. Using a sample from the luxury segment of the hotel industry, this study provides preliminary results supporting a holistic approach to hospitality customers’ postpurchase decision-making process. The model appears to possess practical validity as well as explanatory ability. Implications are discussed and suggestions are developed for both marketers and researchers. ( 1999 Elsevier Science Ltd. All rights reserved.
The Anachronism of the Work Ethic

Review of All the Livelong Day: The Meaning and Demeaning of Routine Work by Barbara Garson; Working: People Talk About What They Do and How They Feel About What They Do by Studs Terkel. This article can also be found at the Monthly Review website , where most recent articles are published in full. Click here to purchase a PDF version of this article at the Monthly Review website.
Design of an Underactuated Compliant Gripper for Surgery using Nitinol

This paper presents the development of an underactuated compliant gripper using a biocompatible super elastic alloy, namely Nitinol. This gripper has two ngers with ve phalanges each and can be used as the end-e ector of an endoscopic instrument. Optimization procedures are required to obtain the geometry of the transmission mechanism because of its underactuated nature and its underlying complexity. A driving mechanism further incorporated in the gripper to distribute actuation to both ngers and accomplish the grasping of asymmetrical objects without requiring supplementary inputs is also discussed. Finally, the results of numerical simulations with di erent materials and di erent grasped objects are presented and discussed. ∗e-mail: mario.doria@polymtl.ca †Corresponding author: Deparment of Mechanical Engineering, École Polytechnique de Montréal, Montréal, QC, H3T 1J4, Canada, phone: 514-340-4711 #3329; fax: 514-340-5867; e-mail: lionel.birglen@polymtl.ca 1 Pr ep rin t o f a pa pe r fr om th e A SM E Jo urn al of Me dic al De vic es , V ol. 3, no . 1 , M arc h 2 00 9.
Interspace between Popliteal Artery and posterior Capsule of the Knee (IPACK) Injectate Spread: A Cadaver Study.

OBJECTIVES
Local anesthetic injection into the interspace between the popliteal artery and the posterior capsule of the knee (IPACK) has the potential to provide motor-sparing analgesia to the posterior knee after total knee arthroplasty. The primary objective of this cadaveric study was to evaluate injectate spread to relevant anatomic structures with IPACK injection.


METHODS
After receipt of Institutional Review Board Biospecimen Subcommittee approval, IPACK injection was performed on fresh-frozen cadavers. The popliteal fossa in each specimen was dissected and examined for injectate spread.


RESULTS
Ten fresh-frozen cadaver knees were included in the study. Injectate was observed to spread in the popliteal fossa at a mean ± SD of 6.1 ± 0.7 cm in the medial-lateral dimension and 10.1 ± 3.2 cm in the proximal-distal dimension. No injectate was noted to be in contact with the proximal segment of the sciatic nerve, but 3 specimens showed injectate spread to the tibial nerve. In 3 specimens, the injectate showed possible contact with the common peroneal nerve. The middle genicular artery was consistently surrounded by injectate.


CONCLUSIONS
This cadaver study of IPACK injection demonstrated spread throughout the popliteal fossa without proximal sciatic involvement. However, the potential for injectate to spread to the tibial or common peroneal nerve was demonstrated. Consistent surrounding of the middle genicular artery with injectate suggests a potential mechanism of analgesia for the IPACK block, due to the predictable relationship between articular sensory nerves and this artery. Further study is needed to determine the ideal site of IPACK injection.
Participatory design in community informatics

Participatory design e the direct involvement of end-users and other stakeholders in design e has become a standard design paradigm in informatics, that is, in developing information systems, applications, infrastructures, and associated work practices. Community informatics, which addresses the impacts and utilisation of information technology to facilitate community life, is a challenging, but important domain for further developing participatory design. 2007 Elsevier Ltd. All rights reserved.
Evaluation of hand bone loss by digital X-ray radiogrammetry as a complement to clinical and radiographic assessment in early rheumatoid arthritis: results from the SWEFOT trial

BACKGROUND
To investigate hand bone loss (HBL) measured by digital X-ray radiogrammetry (DXR) in patients with early rheumatoid arthritis (RA) receiving different treatment regimens, and to evaluate if DXR change rates during the first 12 months correlate with radiological damage after 24 months.


METHODS
From the total SWEFOT trial population, 159 patients had hand radiographs correctly timed and taken with same modality to be analyzed with DXR. All patients started treatment with methotrexate. After 3-4 months, patients with DAS28 > 3.2 were randomized to add sulfasalazine and hydroxychloroquine (triple therapy) or infliximab (MTX + INF). Those with DAS28 ≤3.2 were followed in regular care. Radiographic progression over 24 months was scored according to the Sharp van der Heijde score (SHS) and defined as >5 increase in T-SHS over 24 months. Hand bone mineral density (BMD) was measured by DXR at inclusion and 12 months and a change ≥2.5 mg/cm2/month was used as a cut-off for HBL.


RESULTS
In the MTX responders, triple therapy, and MTX + INF groups, the proportions with HBL were 4.1%, 22.2% and 16.4%, respectively (p = 0.01), and the mean (SD) radiological progression in these groups was 3.91 (6.72), 7.40 (14.63) and 2.72 (4.55) respectively (p = 0.06). Patients with HBL had significantly greater risk for radiographic progression, compared with patients without HBL (odds ratio 3.09, 95% CI =1.20-7.79, p = 0.02).


CONCLUSIONS
Non-responders to MTX had a significantly greater risk of HBL than MTX-responders, despite the add-on therapies. Patients with HBL during the 12 months had greater risk of radiographic progression after 24 months. Evaluation of HBL may help to identify patients who are at risk of radiographic progression.
Awareness of cancer symptoms and anticipated help seeking among ethnic minority groups in England

Objective:Little is known about ethnic differences in awareness of cancer-warning signs or help-seeking behaviour in Britain. As part of the National Awareness and Early Diagnosis Initiative (NAEDI), this study aimed to explore these factors as possible contributors to delay in cancer diagnosis.Methods:We used quota sampling to recruit 1500 men and women from the six largest minority ethnic groups in England (Indian, Pakistani, Bangladeshi, Caribbean, African and Chinese). In face-to-face interviews, participants completed the newly developed cancer awareness measure (CAM), which includes questions about warning signs for cancer, speed of consultation for possible cancer symptoms and barriers to help seeking.Results:Awareness of warning signs was low across all ethnic groups, especially using the open-ended (recall) question format, with lowest awareness in the African group. Women identified more emotional barriers and men more practical barriers to help seeking, with considerable ethnic variation. Anticipated delay in help seeking was higher in individuals who identified fewer warning signs and more barriers.Conclusions:The study suggests the need for culturally sensitive, community-based interventions to raise awareness and encourage early presentation.
A Rare Entity Causing Chronic Sinusitis: Ectopic Tooth in Maxillary Sinus

Ectopic teeth have been rarely described in non-dental and non-oral localizations. Ectopic tooth eruption in maxillary sinus usually runs across incidentally during routine radiological or clinical evaluation because it is generally asymptomatic. If it occurs symptomaticaly; the findings like purulent rhinorrhoea, facial pain, headache, swelling, epistaxis and epiphora can be seen. It is often treated via Caldwell-Luc procedure. In this study, a case of ectopic maxillary third molar tooth on right maxillary sinus is presented.
3M syndrome: an easily recognizable yet underdiagnosed cause of proportionate short stature.

OBJECTIVE
To characterize, via clinical and molecul criteria, a cohort of patients with 3M syndrome and thereby increase awareness of this syndrome as a recognizable cause of proportionate short stature.


STUDY DESIGN
We conducted a case series of patients referred to clinical genetics for proportionate short stature. CUL7, OBSL1, and CCDC8 genes were clinically phenotyped and sequenced.


RESULTS
In 6 Saudi families with 3M syndrome, we identified three CUL7, one OBSL1, and one CCDC8 novel mutations, which we show result in a remarkably similar clinical phenotype. Despite their typical and easily discernible clinical phenotype, all these patients have been extensively investigated for alternative causes of their short stature and received erroneous diagnoses.


CONCLUSION
Increased awareness about this syndrome among pediatricians and endocrinologists is needed to avoid a costly and unnecessary diagnostic odyssey.
High Step-up Boost Converter Integrated With a Transformer-Assisted Auxiliary Circuit Employing Quasi-Resonant Operation

Stacking an auxiliary step-up circuit on top of a boost converter is one of the most attractive structures for nonisolated high step-up applications. In this paper, in order to avoid the large input current ripple of coupled-inductor-based circuits, an auxiliary step-up circuit is integrated via an additional transformer and its balancing capacitor. A voltage-doubler is adopted as an auxiliary step-up circuit, which is inherently suitable for high-voltage applications due to its simple structure and low-voltage stress. Moreover, the transformer leakage inductor and the balancing capacitor constitute a resonant tank so that the quasi-resonant operation makes the current sinusoidal. As a result, a reduced switch turn-off loss and reverse recovery of the diode can be expected. The proposed converter is verified with a 24 V input, 160 W - 200 V output prototype.
Inter-coder agreement for ICD-9-CM coding of stroke

The objective was to evaluate agreement among neurologists for coding stroke, using the International Classification of Diseases 9th Revision – Clinical Modification (ICD-9-CM). Clinical records of 53 consecutive patients (27 stroke or TIA and 26 other diseases) discharged from our general neurology department were coded by four neurology residents, four general neurologists and four neurologists trained in ICD-coding (experts). Inter-coder agreement was evaluated by the kappa statistic. The overall kappa value for coding 430–438 was 0.77 (95% confidence interval 0.70–0.84) for primary (PDx) and 0.82 (0.77–0.88) for PDx+secondary diagnoses (SDx). It was 0.73–0.86 for the residents, 0.78–0.90 for the neurologists and 0.67–0.88 for the experts. The overall kappa values (PDx, SDx) for specific codes were 0.83–0.88 for 431-intracerebral haemorrhage (residents: 0.75–0.89; neurologists: 0.91–0.96; experts: 0.78–0.88) and 0.48–0.51 for 434-occlusion of cerebral arteries) (residents: 0.26–0.26; neurologists: 0.61–0.66; experts: 0.60–0.65). Agreement was substantial for the whole code group 430–438 and higher for code 431 than 434. Reliability was generally improved when both PDx and SDx were considered. Specific training did not increase inter-coders' agreement.
Microstructure and oxidation resistance of C-AlPO4–mullite coating prepared by hydrothermal electrophoretic deposition for SiCC/C composites

Abstract Oxidation resistant C-AlPO 4 –mullite coating for SiC pre-coated carbon/carbon composites (SiCC/C) was prepared by a novel hydrothermal electrophoretic deposition process. The phase composition, surface and cross-section microstructure of the as-prepared multi-layer coatings were characterized by X-ray Diffraction (XRD), scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS). The influence of deposition voltage on phase composition, microstructure and oxidation resistance of the as-prepared coatings was particularly investigated. Results show that the outer layer coating mainly composed of C-AlPO 4 and mullite phase can be achieved after the hydrothermal electrophoretic deposition. The thickness, density and anti-oxidation property of the C-AlPO 4 –mullite coating was improved with the increase of deposition voltage from 160 V to 200 V. The multi-layer coating prepared at a voltage of 200 V exhibit excellent anti-oxidation property, which can effectively protect C/C composites from oxidation in air at 1773 K for 324 h with a weight loss of 1.01%. The failure of the multi-layer coatings is due to the generation of cross-holes in the coating, which cannot be self-cured by the metaphosphate and silicate glass layer after long time oxidation at 1773 K.
Street crossing behavior in younger and older pedestrians: an eye- and head-tracking study

BACKGROUND
Crossing a street can be a very difficult task for older pedestrians. With increased age and potential cognitive decline, older people take the decision to cross a street primarily based on vehicles' distance, and not on their speed. Furthermore, older pedestrians tend to overestimate their own walking speed, and could not adapt it according to the traffic conditions. Pedestrians' behavior is often tested using virtual reality. Virtual reality presents the advantage of being safe, cost-effective, and allows using standardized test conditions.


METHODS
This paper describes an observational study with older and younger adults. Street crossing behavior was investigated in 18 healthy, younger and 18 older subjects by using a virtual reality setting. The aim of the study was to measure behavioral data (such as eye and head movements) and to assess how the two age groups differ in terms of number of safe street crossings, virtual crashes, and missed street crossing opportunities. Street crossing behavior, eye and head movements, in older and younger subjects, were compared with non-parametric tests.


RESULTS
The results showed that younger pedestrians behaved in a more secure manner while crossing a street, as compared to older people. The eye and head movements analysis revealed that older people looked more at the ground and less at the other side of the street to cross.


CONCLUSIONS
The less secure behavior in street crossing found in older pedestrians could be explained by their reduced cognitive and visual abilities, which, in turn, resulted in difficulties in the decision-making process, especially under time pressure. Decisions to cross a street are based on the distance of the oncoming cars, rather than their speed, for both groups. Older pedestrians look more at their feet, probably because of their need of more time to plan precise stepping movement and, in turn, pay less attention to the traffic. This might help to set up guidelines for improving senior pedestrians' safety, in terms of speed limits, road design, and mixed physical-cognitive trainings.