LLukas22/scidocs huggingface dataset:
Impact of QTL properties on the accuracy of multi-breed genomic prediction

Although simulation studies show that combining multiple breeds in one reference population increases accuracy of genomic prediction, this is not always confirmed in empirical studies. This discrepancy might be due to the assumptions on quantitative trait loci (QTL) properties applied in simulation studies, including number of QTL, spectrum of QTL allele frequencies across breeds, and distribution of allele substitution effects. We investigated the effects of QTL properties and of including a random across- and within-breed animal effect in a genomic best linear unbiased prediction (GBLUP) model on accuracy of multi-breed genomic prediction using genotypes of Holstein-Friesian and Jersey cows. Genotypes of three classes of variants obtained from whole-genome sequence data, with moderately low, very low or extremely low average minor allele frequencies (MAF), were imputed in 3000 Holstein-Friesian and 3000 Jersey cows that had real high-density genotypes. Phenotypes of traits controlled by QTL with different properties were simulated by sampling 100 or 1000 QTL from one class of variants and their allele substitution effects either randomly from a gamma distribution, or computed such that each QTL explained the same variance, i.e. rare alleles had a large effect. Genomic breeding values for 1000 selection candidates per breed were estimated using GBLUP modelsincluding a random across- and a within-breed animal effect. For all three classes of QTL allele frequency spectra, accuracies of genomic prediction were not affected by the addition of 2000 individuals of the other breed to a reference population of the same breed as the selection candidates. Accuracies of both single- and multi-breed genomic prediction decreased as MAF of QTL decreased, especially when rare alleles had a large effect. Accuracies of genomic prediction were similar for the models with and without a random within-breed animal effect, probably because of insufficient power to separate across- and within-breed animal effects. Accuracy of both single- and multi-breed genomic prediction depends on the properties of the QTL that underlie the trait. As QTL MAF decreased, accuracy decreased, especially when rare alleles had a large effect. This demonstrates that QTL properties are key parameters that determine the accuracy of genomic prediction.
Microvascular free flap reconstruction versus palatal obturation for maxillectomy defects.

BACKGROUND
Palatal obturators and microvascular free flaps are both used to treat patients with maxillectomy defects, however, the optimal technique remains controversial.


METHODS
A retrospective analysis of 113 patients undergoing maxillectomy for cancer was performed. Seventy-three patients received an obturator and 40 patients were reconstructed with a free flap.


RESULTS
Speech intelligibility and postoperative diet were comparable between the obturator and free flap groups, except in cases of extensive (>50%) palatal defects, where free flap reconstruction was superior in both aspects (p = .019 and p = .043, respectively). The average time for presenting with a local recurrence in advanced cancer involving the palate was comparable in both groups (p = .33).


CONCLUSION
Moderate-sized maxillectomy defects involving the palate can be successfully treated with either an obturator or free flap reconstruction. Extensive defects have a better functional outcome with free flaps. Evidence does not suggest that free flap reconstructions delay diagnosis of local recurrences.
Scaphoid fracture: pediatric emergency care.

PHYSICAL EXAMINATION Tenderness and swelling of the right wrist with poor range of motion on wrist extension and preservation of digital motion were noted. Sensation was normal along the medial, radial, and ulnar nerve distributions, and strong pulses were palpated. VITAL SIGNS Vital signs were stable and within reference limits for age. Wrist radiography was ordered by the emergency department physician under the clinical indication Bwrist pain[ and was performed with standard anteroposterior, oblique, and lateral projections. Standard views were interpreted as normal, and the patient was discharged with in a soft cast and instructed to treat the injury conservatively (outside films were not available for review). During the next week, the pain persisted, and the patient obtained a follow-up visit to a local orthopedist who ordered dedicated Bscaphoid views[ of the wrist to exclude an occult scaphoid fracture (Figs. 1A, B). Dedicated views of the scaphoid demonstrated a nondisplaced fracture through the body of the scaphoid (arrow) without dislocation or periosteal reaction.
Adaptive visualization of search results: Bringing user models to visual analytics

Received: 18 March 2009 Revised: 18 March 2009 Accepted: 20 April 2009 Abstract Adaptive visualization is a new approach at the crossroads of user modeling and information visualization. Taking into account information about a user, adaptive visualization attempts to provide user-adapted visual presentation of information. This paper proposes Adaptive VIBE, an approach for adaptive visualization of search results in an intelligence analysis context. Adaptive VIBE extends the popular VIBE visualization framework by infusing user model terms as reference points for spatial document arrangement and manipulation. We explored the value of the proposed approach using data obtained from a user study. The result demonstrated that user modeling and spatial visualization technologies are able to reinforce each other, creating an enhanced level of user support. Spatial visualization amplifies the user model's ability to separate relevant and non-relevant documents, whereas user modeling adds valuable reference points to relevance-based spatial visualization. Information Visualization (2009) 8, 167--179. doi:10.1057/ivs.2009.12
Gender Differences in Radiation Dose From Nuclear Cardiology Studies Across the World: Findings From the INCAPS Registry.

OBJECTIVES
The aim of this study was to investigate gender-based differences in nuclear cardiology practice globally, with a particular focus on laboratory volume, radiation dose, protocols, and best practices.


BACKGROUND
It is unclear whether gender-based differences exist in radiation exposure for nuclear cardiology procedures.


METHODS
In a large, multicenter, observational, cross-sectional study encompassing 7,911 patients in 65 countries, radiation effective dose was estimated for each examination. Patient-level best practices relating to radiation exposure were compared between genders. Analysis of covariance was used to determine any difference in radiation exposure according to gender, region, and the interaction between gender and region. Linear, logistic, and hierarchical regression models were developed to evaluate gender-based differences in radiation exposure and laboratory adherence to best practices. The study also included the United Nations Gender Inequality Index and Human Development Index as covariates in multivariable models.


RESULTS
The proportion of myocardial perfusion imaging studies performed in women varied among countries; however, there was no significant correlation with the Gender Inequality Index. Globally, mean effective dose for nuclear cardiology procedures was only slightly lower in women (9.6 ± 4.5 mSv) than in men (10.3 ± 4.5 mSv; p < 0.001), with a difference of only 0.3 mSv in a multivariable model adjusting for patients' age and weight. Stress-only imaging was performed more frequently in women (12.5% vs. 8.4%; p < 0.001); however, camera-based dose reduction strategies were used less frequently in women (58.6% vs. 65.5%; p < 0.001).


CONCLUSIONS
Despite significant worldwide variation in best practice use and radiation doses from nuclear cardiology procedures, only small differences were observed between genders worldwide. Regional variations noted in myocardial perfusion imaging use and radiation dose offer potential opportunities to address gender-related differences in delivery of nuclear cardiology care.
OldGen: mobile phone personalization for older adults

Mobile devices are currently difficult to customize for the usability needs of elderly users. The elderly are instead referred to specially designed "senior phones" or software add-ons. These tend to compromise in functionality as they attempt to solve many disabilities in a single solution.
 We present OldGen, a prototype framework where a novel concept enables accessibility features on generic mobile devices, by decoupling the software user interface from the phone's physical form factor. This opens up for better customization of the user interface, its functionality and behavior, and makes it possible to adapt it to the specific needs of each individual. OldGen makes the user interface portable, such that it could be moved between different phone hardware, regardless of model and brand. Preliminary observations and evaluations with elderly users indicate that this concept could address individual user interface related accessibility issues on general-purpose devices.
Comparison of energy efficiency between variable refrigerant flow systems and ground source heat pump systems - eScholarship

With the current movement toward net zero energy buildings, many technologies are promoted with emphasis on their superior energy efficiency. The variable refrigerant flow (VRF) and ground source heat pump (GSHP) systems are probably the most competitive technologies among these. However, there are few studies reporting the energy efficiency of VRF systems compared with GSHP systems. In this article, a preliminary comparison of energy efficiency between the air-source VRF and GSHP systems is presented. The computer simulation results show that GSHP system is more energy efficient than the air-source VRF system for conditioning a small office building in two selected US climates. In general, GSHP system is more energy efficient than the air-source VRV system, especially when the building has significant heating loads. For buildings with less heating loads, the GSHP system could still perform better than the airsource VRF system in terms of energy efficiency, but the resulting energy savings may be marginal.
Results after arthroscopic treatment of central traumatic lesions of the triangular fibrocartilage complex

Injuries of the triangular fibrocartilage complex (TFCC) are of high clinical relevance; however, the clinical evidence for treatment is poor and long-term results are rarely published. The purpose of this study was to evaluate the clinical outcome of symptomatic central traumatic lesions of the TFCC (Palmer 1A) following arthroscopic debridement. Between 2007 and 2013, 87 patients were arthroscopically diagnosed with Palmer 1A lesion and accordingly treated with debridement. Follow-up was available for 43 patients. Activities of daily living (ADLs) were measured with the Disabilities of the Arm, Shoulder and Hand (DASH) questionnaire. Pain perception was evaluated with visual analogue scale (VAS 0–10). Grip strength and wrist motion were assessed with conventional techniques using a Jamar dynamometer and a goniometer. Patient satisfaction was assessed using a questionnaire at follow-up. Mean follow-up was 42.5 months (range 5–70). The mean age of the patients (22 male and 21 female) at time of surgery was 41 ± 15.9 years. No major complication occurred during surgery and follow-up. The DASH score (preoperatively 49.8 ± 19.3 vs. postoperatively 14.1 ± 17.9, p < 0.05) and pain perception (VAS: preoperatively 7.2 ± 2.0 vs. postoperatively 1.4 ± 1.6, p < 0.05) improved significantly. Grip strength was satisfactory after surgery (19.6 ± 13.1). Ulnar deviation improved significantly from 29.3 ± 10.4° to 35.6 ± 8.3° (p < 0.05) and wrist flexion improved from 53.8 ± 18.9° to 67.4 ± 12.9° (p < 0.05). Wrist extension, radial deviation, pronation and supination did not change significantly after surgery. Improved symptoms were reported by 41/43 (95.3%) patients and 40/43 (93%) patients would have had the same procedure again knowing the final outcome. Six of 43 patients (15%) had an ulnar plus variance. None of these needed ulnar shortening. Central traumatic TFCC lesions can safely be treated by arthroscopic debridement. We showed a sustained pain relief with significantly improved quality of life (DASH score) and wrist motion at follow-up. This resulted in a high patient satisfaction and acceptance of the procedure. Therapeutic, level IV.
International Olympic Committee (IOC) Consensus Statement on Relative Energy Deficiency in Sport (RED-S): 2018 Update.

Note. This article has been co-published in the British Journal of Sports Medicine (doi:10.1136/bjsports-2018-099193). Mountjoy is with the Department of Family Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Canada. Sundgot-Borgen is with the Department of Sports Medicine, The Norwegian School of Sport Sciences, Oslo, Norway. Burke is with Sports Nutrition, Australian Institute of Sport, Belconnen, Australia, and Centre for Exercise and Nutrition, Mary MacKillop Institute for Health Research, Melbourne, Australia. Ackerman is with the Divisions of Sports Medicine and Endocrinology, Boston Children’s Hospital and the Neuroendocrine Unit, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts. Blauwet is with the Department of Physical Medicine and Rehabilitation, Harvard Medical School, Spaulding Rehabilitation Hospital/Brigham and Women’s Hospital, Boston, Massachusetts. Constantini is with the Heidi Rothberg Sport Medicine Center, Shaare Zedek Medical Center, Hebrew University, Jerusalem, Israel. Lebrun is with the Department of Family Medicine, Faculty of Medicine & Dentistry, and Glen Sather Sports Medicine Clinic, University of Alberta, Edmonton, Alberta, Canada. Melin is with the Department of Nutrition, Exercise and Sport, University of Copenhagen, Frederiksberg, Denmark. Meyer is with the Health Sciences Department, University of Colorado, Colorado Springs, Colorado. Sherman is a counselor in Bloomington, Indiana. Tenforde is with the Department of Physical Medicine and Rehabilitation, Harvard Medical School, Spaulding Rehabilitation Hospital, Charlestown, Massachusetts. Klungland Torstveit is with the Faculty of Health and Sport Sciences, University of Agder, Kristiansand, Norway. Budgett is with the IOC Medical and Scientific Department, Lausanne, Switzerland. Address author correspondence to Margo Mountjoy at mmsportdoc@mcmaster.ca. Margo Mountjoy McMaster University
Quay crane scheduling with non-interference constraints in port container terminals

Nowadays competition between port container terminals, especially between geographically close ones, is rapidly increasing. How to improve the competitiveness of port container terminals is, therefore, an immediate challenge, with which port operators are confronted. In terms of port competitiveness, the makespan of a container vessel, which is the latest completion time among all handling tasks of the container vessel, is a critical success factor (Steenken et al., 2004). In reality, quay crane scheduling significantly affects the makespan of a container vessel since quay cranes are the interface between land side and water side in any port container terminals. Thus this paper aims to study quay crane scheduling problem to enhance the competitiveness of port container terminals.
Initial and Late Results of Freedom Coronary Stent

OBJECTIVES
Initial and late results after implantation of Freedom stents, a balloon expandable stainless steel coil stents were evaluated.


METHODS
From Jun. 1996 to Nov. 1997, we implanted 123 Freedom stents in 122 lesions in 117 patients and performed follow-up coronary angiograms at 7.0 +/- 3.6 months after stents placement. Clinical courses after stenting and follow-up coronary angiographic findings were evaluated. Comparison of clinical, angiographic, and procedural factors according to the presence or absence of restenosis was performed.


RESULTS
In 117 patients who underwent stents implantation, major complications were not observed. Follow-up coronary angiograms were performed in 47 stents in 41 patients (35%). Among 47 stents, angiographic significant restenosis (percent diameter stenosis > 50%) was observed in 13 (28%). Mean age in 41 patients was 59 +/- 9 years, with 27 male patients (66%). Indications for stents implantation were de novo lesions in 18 (38%), suboptimal results after PTCA in 18 (38%), bail-out lesions in 4 (9%) and restenotic lesions in 7 (15%). Lesion types by AHA/ACC classification were A in 1 (1%), B1 in 10 (21%), B2 in 17 (36%), and C in 19 (40%). Average lesion length was 13.7 +/- 9.0 mm, stent diameter 3.0 +/- 0.3 mm, and stent length 24.6 +/- 9.0 mm. There were no significant differences of the clinical, angiographic, and procedural characteristics according to the presence or absence of restenosis.


CONCLUSION
Freedom coronary stents implantation is safely performed in various morphology of coronary lesions and no significant predictive factors on restenosis in follow-up coronary angiogram were observed.
'Black dots' seen under trichoscopy are not specific for alopecia areata.

BACKGROUND
'Black dots' are macrocomedo-like round structures localized to the follicular ostium, and are considered a specific trichoscopic feature of alopecia areata (AA).


AIM
To characterize specific features of 'black dots', and assess their possible presence in common hair and scalp disorders.


METHODS
In total, 107 patients with hair loss [30 with alopecia areata (AA), 37 with androgenetic alopecia (AGA), 17 with chronic telogen effluvium (TE), 23 with other hair and scalp diseases] and 93 healthy controls were examined, using a videodermoscope with 20-70 times magnification.


RESULTS
There was a correlation between the black dots and the early acute phase of the various alopecia types with the presence of the black dots. Black dots were found in 11% (22/107) of patients with hair loss, including 53.3% (16/30) with AA; in 40% (2/5) of patients with severe chemotherapy-induced alopecia, and in 100% of patients with dissecting cellulitis of the scalp (n = 2), hypotrichosis simplex (n = 1), and congenital aplasia cutis (n = 1). No black dots were seen in patients with AGA or TE.


CONCLUSIONS
Black dots are not specific for AA, and may be present in other hair and scalp diseases.
Cost model based service placement in federated hybrid clouds

As cloud federation allows companies in need of computational resources to use computational resources hosted by different cloud providers, it reduces the cost of IT infrastructure by lowering capital and operational expenses. This is the result of economies of scale and the possibility for organizations to purchase just as much computing and storage resources as needed whenever needed. However, a clear specification of cost savings requires a detailed specification of the costs incurred. Although there are some efforts to define cost models for clouds, the need for a comprehensive cost model, which covers all cost factors and types of clouds, is undeniable. In this paper, we cover this gap by suggesting a cost model for the most general form of a cloud, namely federated hybrid clouds. This type of cloud is composed of a private cloud and a number of interoperable public clouds. The proposed cost model is applied within a cost minimization algorithm for making service placement decisions in clouds. We demonstrate the workings of our cost model and service placement algorithmwithin a specific cloud scenario. Our results show that the service placement algorithmwith the costmodelminimizes the spending for computational services. © 2014 Elsevier B.V. All rights reserved.
Research Challenges for the Security of Control Systems

In this paper we attempt to answer two questions: (1) Why should we be interested in the security of control systems? And (2) What are the new and fundamentally different requirements and problems for the security of control systems? We also propose a new mathematical framework to analyze attacks against control systems. Within this framework we formulate specific research problems to (1) detect attacks, and (2) survive attacks.
PAP: A privacy and authentication protocol for passive RFID tags

Passive Radio Frequency Identification (RFID) tags, due to their ability to uniquely identify every individual item and low cost, are well suited for supply chain management and are expected to replace barcodes in the near future. However, unlike barcodes, these tags have a longer range in which they are allowed to be scanned, subjecting them to unauthorized scanning by malicious readers and to various other attacks, including cloning attacks. Therefore, a security protocol for RFID tags is necessary to ensure the privacy and authentication between each tag and their reader. In order to accomplish this, we propose PAP, a privacy and authentication protocol for passive RFID tags. This protocol requires little computation and achieves both privacy and authentication, making it sufficient enough for use in supply chain management; however, this protocol is also suitable for use in other RFID applications as well.
Effect of effective lens position on cylinder power of toric intraocular lenses.

OBJECTIVE
To evaluate the effects of effective lens position (ELP) on the corneal plane effective cylinder power of toric intraocular lenses (IOLs).


DESIGN
Retrospective cross-sectional study.


PARTICIPANTS
Ninety-four eyes from 78 patients who underwent uncomplicated phacoemulsification with implantation of an AcrySof toric IOL (1.50- to 3.00-D cylinder).


METHODS
The amount of corneal plane effective cylinder power of toric IOLs given by the manufacturer (target-induced astigmatism vector [TIA]) was compared with the postoperatively achieved cylindrical correction (surgically induced astigmatism vector [SIA]). The theoretical corneal plane cylinder power of toric IOLs was calculated according to ELP and corneal power using a refractive vergence formula.


RESULTS
The TIA (1.59 ± 0.43 D) was significantly smaller than the SIA (1.78 ± 0.65 D; p < 0.001). The difference between the magnitudes of SIA and TIA demonstrated a significant negative correlation with ELP (r = -0.219 and p = 0.034). The theoretical corneal plane cylinder power of toric IOLs demonstrated a decreasing trend as the ELP and corneal power increased. The range of changes in corneal plane effective cylinder power according to ELP and corneal power was greater in toric IOLs with high toricity.


CONCLUSIONS
The cylinder power of AcrySof toric IOLs should be adjusted according to ELP. For eyes with small ELP, the cylinder power should be reduced, and for eyes with large ELP, the cylinder power should be increased. The amount of reducing or increasing cylinder power of toric IOLs should be increased as the toricity increases.