Miracle-dz/UniFAR-FTUs huggingface dataset:
De novo peptide sequencing using CID and HCD spectra pairs

In tandem mass spectrometry (MS/MS), there are several different fragmentation techniques possible, including, collision‐induced dissociation (CID) higher energy collisional dissociation (HCD), electron‐capture dissociation (ECD), and electron transfer dissociation (ETD). When using pairs of spectra for de novo peptide sequencing, the most popular methods are designed for CID (or HCD) and ECD (or ETD) spectra because of the complementarity between them. Less attention has been paid to the use of CID and HCD spectra pairs. In this study, a new de novo peptide sequencing method is proposed for these spectra pairs. This method includes a CID and HCD spectra merging criterion and a parent mass correction step, along with improvements to our previously proposed algorithm for sequencing merged spectra. Three pairs of spectral datasets were used to investigate and compare the performance of the proposed method with other existing methods designed for single spectrum (HCD or CID) sequencing. Experimental results showed that full‐length peptide sequencing accuracy was increased significantly by using spectra pairs in the proposed method, with the highest accuracy reaching 81.31%.
Explaining the desire for local bargaining: Evidence from a Finnish survey of employers and employees

The aim of this paper is to describe divergences in employers’ and employees’ opinions on the proper share of local bargaining in contract wage gains, and explain when these divergences are particularly large or small. The paper shows that employers want the locally bargained wage share to be approximately half of the total wage rise, while the majority of employees would prefer this share to be in the region of 1-24%. Employers in firms that are large or operate in the financial services industry desire the largest locally bargained share of contract wages. Employees in large firms are, instead, afraid of losing their bargaining power and tend to resist local bargaining. Employees in firms with profit sharing plans believe that local bargaining should be afforded a large role. It is likely that employer and employees agree on not having much local bargaining in firms that operate in an uncompetitive product market and that they agree on substantial local bargaining in firms that are domestically owned and whose majority of employees work abroad. JEL: J31, J59, C24
Energy efficient routing protocol for ambient assisted living environment with multiple sinks

In the last few years Ambient Assisted Living (AAL) has come up a long way with numerous innovative ideas to cater to the growing elderly population of the society. With a perfect combination of tools and technology leading to ubiquitous or pervasive computing, data can be sensed, and transmitted from patients at home to healthcare professionals for quick monitoring and taking necessary actions, if needed. Existing routing protocols have been successfully implemented using single sink WBAN. In order to ensure proper communication between patients and their caregivers, in this paper we focus on a multi-sink approach that can improve the efficiency and effectiveness of AAL to a greater extent. The routing protocol proposed in this work always chooses the most suitable sink (single hop) or a forwarder (multi hop) despite relative node mobility thus providing an improved architecture for AAL. The protocol is simulated. Results show that the proposed protocol achieves better energy efficiency. When compared with state-of-the art protocols, it gives better throughput in terms of number of received packets.
BelliesWave: color and shape changing pixels using bilayer rubber membranes

classroom use is granted without fee provided that copies are not made or distributed for commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the Owner/Author. SIGGRAPH 2014, August 10 – 14, 2014, Vancouver, British Columbia, Canada. 2014 Copyright held by the Owner/Author. ACM 978-1-4503-2958-3/14/08 BelliesWave: Color and Shape Changing Pixels Using Bilayer Rubber Membranes
Water Intake and NaCl Appetite in Sodium Depletion

Rats were sodium depleted by intraperitoneal dialysis (IPD) to determine: (a) whether there is a thirst mechanism not dependent on increases in effective osmotic pressure and (b) whether a sodium chloride appetite could be induced by this rapid means of sodium depletion. IPD resulted in increased intakes of water and 3% NaCl solution when these were tested independently (single-stimulus method) A second IPD performed after 2 days of recovery produced even greater increases in intake. When water and 3% NaCl were available simultaneously after both dialyses, the increased salt intake was shown to be the predominant effect. The increased water intake occurred in spite of cellular overhydration and decreased serum Na level.
The National Cancer Data Base: Ten years of growth and commitment

The National Cancer Data Base (NCDB), now 10 years old, was created to provide a resource for assessing patient care and outcomes nationally and to circulate this information to the medical community. Dr. Partridge says the NCDB clearly has succeeded in fulfilling this and other goals and can be expected to continue to be an important source for evaluating patterns of cancer care in the United States.
Arabic Named Entity Recognition

Tesis doctoral en Informatica realizada por Yassine Benajiba y dirigida por el doctor Paolo Rosso (Univ. Politecnica de Valencia). El acto de defensa de tesis tuvo lugar en Valencia en Mayo de 2009 ante el tribunal formado por los doctores Felisa Verdejo (UNED), Mona Diab (Columbia Univ.), Imed Zitouni (IBM T.J. Watson Research Center), Horacio Rodriguez (Univ. Politecnica de Cataluna) y Encarna Segarra (Univ. Politecnica de Valencia). La calificacion obtenida fue So- bresaliente Cum Laude.
Completely automated estimation of prostate volume for 3-D side-fire transrectal ultrasound using shape prior approach

Real-time knowledge of capsule volume of an organ provides a valuable clinical tool for 3D biopsy applications. It is challenging to estimate this capsule volume in real-time due to the presence of speckles, shadow artifacts, partial volume effect and patient motion during image scans, which are all inherent in medical ultrasound imaging. The volumetric ultrasound prostate images are sliced in a rotational manner every three degrees. The automated segmentation method employs a shape model, which is obtained from training data, to delineate the middle slices of volumetric prostate images. Then a "DDC" algorithm is applied to the rest of the images with the initial contour obtained. The volume of prostate is estimated with the segmentation results. Our database consists of 36 prostate volumes which are acquired using a Philips ultrasound machine using a Side-fire transrectal ultrasound (TRUS) probe. We compare our automated method with the semi-automated approach. The mean volumes using the semi-automated and complete automated techniques were 35.16 cc and 34.86 cc, with the error of 7.3% and 7.6% compared to the volume obtained by the human estimated boundary (ideal boundary), respectively. The overall system, which was developed using Microsoft Visual C++, is real-time and accurate.
Sliding Mode Control Applied to Active Suspension Using Nonlinear Full Vehicle and Actuator Dynamics

For the purpose of fault diagnosis and tolerance, a sliding mode controller (SMC) is designed for a nonlinear full vehicle active suspension system. Since actuators are used to generate forces in active suspension, the dynamics of the four electro-hydraulic actuators are taken into consideration. Simulation is made to illustrate the proposed controller where the active suspension system performances are compared to those of passive suspension
Risk Factors for Asthma in School Children from Ciudad Juarez, Chihuahua

Asthma and allergic rhinitis were analyzed in a random sample of school children (n = 6174) residing in Ciudad Juarez, Chihuahua, Mexico. The International Study of Asthma and Allergies in Childhood methodology was applied through a standardized questionnaire. The sample was obtained with a bietapic design. Cumulative prevalence of asthma and wheezing was 6.8% (95% CI 6.2, 7.4) and 20% (95% of CI 19.7, 21.8) respectively; the prevalence of rhinitis was 5.0% (95% CI 4.5, 5.6). Family history of asthma odds ratio (OR) 2.33 (95% CI 1.78–3.05), respiratory infection after birth (OR) 3.44 (95% CI 2.76–4.29), and exposure to environmental tobacco (OR) 1.35 (95% CI 1.06–1.68) were the strongest risk factors for asthma and allergic rhinitis. The multifactorial etiology of asthma and allergic rhinitis was confirmed, as well as the importance of early exposure to environmental factors.
Evaluation of Hardware Oriented MRCoHOG using Logic Simulation

Human detection require high speed and high accuracy processing. One of the high performance techniques of the detection is multi-resolution co-occurrence histogram of oriented gradients (MRCoHOG). Since the calculation of co-occurrence requires a huge amount of processing resources, it is difficult to realize real-time human detection with MRCoHOG. Accordingly, hardware implementation is considered to be effective. In this paper, a hardware oriented MRCoHOG is proposed. In the proposed method, we simplify complicated calculation such as multiplications and square root operation for efficient hardware implementation. Experimental results show that the proposed method achieves better human detection rate than the ordinary method. Moreover, MRCoHOG is implemented in a digital circuit with the proposed method. According to logic simulation of the proposed circuit, the processing speed of the hardware implementation is 466 times higher than the software implementation.
Evaluation of Menopausal Interventions at a Japanese Company

The purpose of this research was to evaluate the impact of interventions for menopausal symptoms among employees at a newspaper company in Japan and to clarify the role of the occupational health nurse. Since 2000, the company has focused on creating a comfortable work environment for its female employees. As part of this effort, this research study also aimed to evaluate a system to support employees experiencing menopausal symptoms. Methods of evaluation included surveys of current employees or former employees with symptoms of menopause and case studies of three women. As a result of these data, it became clear that differentiating between menopausal disorders and mental health issues was not always easy. However, comparisons before and after implementing changes in the health system revealed that the number of women describing symptoms of menopause decreased from 5 to 0, and the number of women retiring, dying while still employed, or taking more than 4 days of sick leave in a month decreased from 3 to 0. This research revealed that interventions for menopause, similar to mental health interventions, require specific human resources and systemic support.
Prognostic value of cell cycle arrest biomarkers in patients at high risk for acute kidney injury: A systematic review and meta‐analysis

Urinary tissue inhibitor of metalloproteinase‐2 (TIMP‐2) and insulin‐like growth factor binding protein 7 (IGFBP7) are G1 cell cycle arrest biomarkers. This systematic review aimed to evaluate the prognostic value of urinary [TIMP‐2]·[IGFBP7] in patients at high risk for AKI. The MEDLINE (via PubMed), Ovid, EMBASE and Cochrane Library databases were systematically searched from inception to December 25, 2016. Original clinical studies which met the eligibility criteria were included in this study. The prognostic accuracy of urinary [TIMP‐2]·[IGFBP7] for assessing the need for renal replacement therapy (RRT) and mortality was evaluated by pooled sensitivity, specificity, diagnostic odds ratio, and summary receiver operating characteristic curves. A total of four prospective cohort studies evaluating 277 patients were included. The estimated area under the receiver operating characteristic curve (AUC) of urinary [TIMP‐2]·[IGFBP7] for predicting the need for RRT in patients at high risk for AKI was 0.915 (standard error [SE] = 0.040). Pooled sensitivity and specificity with corresponding 95% confidence intervals (CI) were 0.69 (95% CI 0.53–0.82) and 0.81 (95% CI 0.75–0.86), respectively. Urinary [TIMP‐2]·[IGFBP7] for mortality prediction in patients at high risk for AKI was assessed by qualitative description. Based on the above data, urinary [TIMP‐2]·[IGFBP7] performs well in predicting the need for RRT and mortality in patients at high risk for AKI. However, further meta‐analyses are warranted as more data become available.
Growth phase of the diatom Skeletonema marinoi influences the metabolic profile of the cells and the selective feeding of the copepod Calanus spp.

Copepods dominate the biomass of marine zooplankton and through their prey selection they act as top-down regulators of planktonic communities. We investigated feeding preference of copepods in the presence of the diatom Skeletonema marinoi at different time points throughout the development of a bloom and a culture. Quantitative PCR gut content assessment revealed that the food uptake of the copepod Calanus spp. on mixed diets and on artificially induced mesocosm blooms was selective. Uptake of S. marinoi was highest during the post-bloom phase in the mesocosms even if the abundance of this alga was already low. In laboratory assays, copepods showed a greater preference for S. marinoi in the late stationary phase than for cultures of the same strain under exponentially growing culture conditions. The copepods thus discriminate between different growth phases of a single algal species in both laboratory and field settings. In parallel, we monitored cellular metabolites of the diatom using a metabolomic approach. Complex changes in the metabolic profile occur during development of a culture. Since no obvious effect of nutrient quality and cell size was involved, we suggest that changes in (info)chemicals within or surrounding S. marinoi regulate selective feeding by zooplankton.
Modeling the Effects of Predation, Prey Cycling, and Time Averaging on Relative Abundance in Raptor-Generated Small Mammal Death Assemblages

Abstract Raptors concentrate the remains of their small mammal prey in pellets rich in skeletal material. Stratified pellet deposits beneath long-term roost sites should, therefore, represent valuable archives of Holocene faunal change. Accurate paleoecological reconstruction from such deposits, however, requires a complete assessment of factors that may bias the ecological information that such records preserve. Three factors that could bias or obscure the community structure of a small mammal death assemblage relative to the living community include: (1) short-term transient dynamics of prey populations; (2) feeding activity of the raptors; and (3) extent of time averaging represented in individual stratigraphic horizons. Here I model (1) how much summed time is necessary for a raptor-derived small mammal death assemblage to capture a long-term (centennial to millennial) signal of relative abundance; and (2) the accuracy of the relative abundance information preserved in such death assemblages given short-term (decadal) cycling of small mammal prey populations. Results generated from an empirically parameterized model of prey dynamics assuming a multi-species type III functional response of raptors to fluctuations in density of two prey species suggest that the maximum extent of time averaging necessary to capture a stable relative abundance signal in a death assemblage is ∼140 years. This estimate is highly conservative, yet still remains fine enough to analyze phenomena operating at the centennial to millennial time scales critical for addressing long-term community response to habitat transitions through the Holocene. Results also suggest that the mismatch between relative abundance information in the living community and the death assemblage is generally low (<1%), except for a few specific parameter combinations that result in the population dynamics of the prey species being extremely similar to one another.
The Effects of School Impact Fees on Commercial and Residential Land Values

Gregory S. Burge, Department of Economics, University of Oklahoma Abstract Development impact fees are a controversial method of financing local public infrastructure. While their effects on home values have been examined extensively, very few studies have investigated how they influence the price of undeveloped land. A 16 year panel is used to investigate the effects of impact fee programs in Florida on the value of residentially and commercially zoned parcels. Three main findings are obtained. First, school impact fee programs decrease the value of residentially zoned land but increase the value of commercially zoned parcels. Second, fees for water and sewer reduce the price of residentially zoned parcels but have no significant effect on commercially zoned land values. Finally, fees for other traditional categories seem to have stronger negative effects on commercially zoned properties than on residential parcels.
Quality Enhancement of 3D Models Reconstructed By RGB-D Camera Systems

QUALITY ENHANCEMENT OF 3D MODELS RECONSTRUCTED BY RGB-D CAMERA SYSTEMS by Chuanbo Wang The University of Wisconsin-Milwaukee, 2015 Under the Supervision of Professor Zeyun Yu Low-cost RGB-D cameras like Microsoft's Kinect capture RGB data for each vertex while reconstructing 3D models from objects with obvious drawbacks of poor mesh and texture qualities due to their hardware limitations. In this thesis we propose a combined method that enhances geometrically and chromatically 3D models reconstructed by RGB-D camera systems. Our approach utilizes Butterfly Subdivision and Surface Fitting techniques to generate smoother triangle surface meshes, where sharp features can be well preserved or minimized by different Surface Fitting algorithms. Additionally the global contrast of mesh textures is enhanced by using a modified Histogram Equalization algorithm, in which the new intensity of each vertex is obtained by applying cumulative distribution function and calculating the accumulated normalized histogram of the texture. A number of experimental results and comparisons demonstrate that our method efficiently and effectively improves the geometric and chromatic quality of 3D models reconstructed from RGB-D cameras.
P.S.* I Love You: Implications of Phosphatidyl Serine (PS) Reversal in Acute Ischemic Syndromes

The concept introduced by Thimister et al. (1) in their investigation of acute myocardial infarction, reported in this issue of The Journal of Nuclear Medicine, is the difference in the mechanism of localization of the radiopharmaceutical annexin A5, compared with that of antimyosin or pyrophosphate (2,3). Both antimyosin and pyrophosphate require loss of integrity of the cell membrane to achieve localization. Annexin A5 localizes to the outer leaflet of the intact membrane of cells expressing phosphatidyl serine (PS). The nanomolar affinity of 99mTc-annexin A5 toward cell membrane– bound PS provides high contrast in the images. Unlike irreversibly damaged myocardium (detected by antimyosin imaging), the apoptotic process may be amenable to intervention, allowing these severely injured cells to survive and continue to contribute to overall ventricular function (2,3). Indeed, significant therapeutic implications can be gleaned from the article of Thimister et al.
Evaluation of an albumin-binding gadolinium contrast agent in multiple sclerosis

Objective: The first goal of this study is to compare gadofosveset trisodium—a gadolinium agent that reversibly binds to albumin—to an extracellular contrast agent (Gd-DOTA) for the detection of multiple sclerosis lesions. The second goal is to determine the best postinjection time for the detection of contrast-enhanced lesions. Methods: Nine patients underwent 2 MRI examinations, respectively, after Gd-DOTA (0.1 mmol/kg) and gadofosveset trisodium (0.03 mmol/kg) administration. Axial T1 spin-echo–weighted images were acquired at several time points after injection (4 minutes for Gd-DOTA, and 4, 8, 12, 16, 20 minutes, 1 hour, and 4 hours for gadofosveset trisodium). Images were analyzed by 4 neuroradiologists who marked the contrast-enhanced lesions and, for each marked lesion, chose the acquisition they preferred and segmented the lesion on their preferred acquisition. Results: The 4-hour gadofosveset trisodium acquisition was ranked best for the 3 tasks: contrast-enhanced lesions were seen by more readers, they preferred this acquisition, and improvements of the signal enhancement (125%) and of the contrast-to-noise ratio (73%) vs Gd-DOTA at 4 minutes were observed (p < 0.05). Conclusion: Gadofosveset trisodium after 4 hours significantly improves the number of detected contrast-enhanced multiple sclerosis lesions as compared to Gd-DOTA after 4 minutes, even though the injected dose of gadolinium was two-thirds lower.
2 D pose estimation in the Restaurant of the Future

This thesis presents the research that has been done on a framework for people tracking in 3D. We developed this framework as a potential product for Noldus IT to evaluate human behaviour in the Restaurant of the Future. We focus on three di erent aspects in the framework: steering pan-tilt-zoom cameras, calibrating these cameras and detecting people and estimating their body poses. We evaluated the functionality of pan-tilt-zoom cameras to see whether they can be used to their full potential in a tracking framework. We concluded that the image quality, even when panning or tilting at a speed which captures walking people, is su cient for pose estimation. A major disadvantage of the PTZ camera is that its accuracy is not high enough for it to be used in our framework. The camera can be in a di erent position and produce di erent images even though it has been sent to the same pan-tilt-zoom state. We researched the calibration of static cameras using Zhang's method [28] and concluded that the convergence of internal parameters is questionable. After that, we looked at auto-calibration techniques such as [18, 23, 24, 27], to keep the cameras calibrated throughout their on-line pan, tilt and zoom movements. We did not nd an auto calibration method immediately suitable for our framework but we did nd interesting approaches that could potentially ful ll this task. In order for this to work we would have to create a 3D model of the scene beforehand. In order to estimate the poses of the people in the scene, we made use of the Pictorial Structures framework presented in [2]. We evaluated the accuracy of the method on di erent datasets and identi ed its strengths and weaknesses. We showed that the amount of correctly estimated bodyparts on di erent datasets is around 55%. Though, the method is too slow to be used in our real-time framework as it takes around 90 minutes on an average PC for a pose estimation on the images produced by our PTZ cameras. We showed that the method could be sped up around 60 times using a faster detection algorithm, at the cost of around 18% accuracy. Still, the pose estimation will take more than a minute thus other speed ups will have to be found to be able to use it in our framework.