nils-herrmann/clean_scirepeval huggingface dataset:
Community challenges in biomedical text mining over 10 years: success, failure and the future

One effective way to improve the state of the art is through competitions. Following the success of the Critical Assessment of protein Structure Prediction (CASP) in bioinformatics research, a number of challenge evaluations have been organized by the text-mining research community to assess and advance natural language processing (NLP) research for biomedicine. In this article, we review the different community challenge evaluations held from 2002 to 2014 and their respective tasks. Furthermore, we examine these challenge tasks through their targeted problems in NLP research and biomedical applications, respectively. Next, we describe the general workflow of organizing a Biomedical NLP (BioNLP) challenge and involved stakeholders (task organizers, task data producers, task participants and end users). Finally, we summarize the impact and contributions by taking into account different BioNLP challenges as a whole, followed by a discussion of their limitations and difficulties. We conclude with future trends in BioNLP challenge evaluations.
Power consumption estimation in CMOS VLSI chips

Power consumption from logic circuits, interconnections, dock distribution, on chip memories, and off chip driving in CMOS VLSI is estimated. Estimation methods are demonstrated and verified. An estimate tool is created. Power consumption distribution between ~ I I ~ I T O M ~ C ~ ~ O I W , clock distribution, logic gates, memories, and off chip driving are analyzed by examples. Comparisons are done between cell library, gate array, and full custom design. Also comparisons between static and dynamic logic are given. Results show that the power consumption of all interconnections and off chip driving can be up to 20% and 65% of the total power consumption respectively. Compared to cell library design, gate array designed chips consume about 10% more power, and power reduction in full custom designed chips could be 15%.
Comparison of surgical variables and short-term postoperative complications in healthy dogs undergoing ovariohysterectomy or ovariectomy.

To determine whether ovariohysterectomy (OVH) required more time to complete and was associated with more short-term postoperative complications than ovariectomy (OVE) in dogs.



Randomized prospective clinical trial.



40 healthy, sexually intact female dogs.


PROCEDURES
OVH (in 20 dogs) or OVE (20 dogs) was performed by use of standardized anesthetic and surgical protocols. Physical characteristics of the dogs, surgical variables, pain scores derived from behavior-based composite pain scales, and surgical wound characteristics were analyzed.



Body weight, age, body condition score, and distance between the sternal manubrium and the pubic rim were comparable among dogs that underwent either surgical procedure. Body weight was positively correlated with the total duration of the procedure and with time required for closure of the surgical wound. No effect of body condition score was determined for any variable. Skin and fascia incision lengths relative to the distance from the sternal manubrium to pubic rim were significantly greater in dogs that underwent OVH, compared with those of dogs that underwent OVE, but total surgical time was not different for the 2 procedures. No other significant differences were detected between the 2 groups.



Significant differences in total surgical time, pain scores, and wound scores were not observed between dogs that underwent OVH and dogs that underwent OVE via standardized protocols.
Experimental study of desalination using direct contact membrane distillation : a new approach to flux enhancement

New membrane distillation configurations and a new membrane module were investigated to improve water desalination. The performances of three hydrophobic microporous membranes were evaluated under vacuum enhanced direct contact membrane distillation (DCMD) with a turbulent flow regime and with a feed water temperature of only 40 ◦C. The new configurations provide reduced temperature polarization effects due to better mixing and increased mass transport of water due to higher permeability through the membrane and due to a total pressure gradient across the membrane. Comparison with previously reported results in the literature reveals that mass transport of water vapors is substantially improved with the new approach. The performance of the new configuration was investigated with both NaCl and synthetic sea salt feed solutions. Salt rejection was greater than 99.9% in almost all cases. Salt concentrations in the feed stream had only a minor effect on water flux. The economic aspects of the enhanced DCMD process are briefly discussed and comparisons are made with the reverse osmosis (RO) process for desalination.
Nurturing brain plasticity: impact of environmental enrichment

Environmental enrichment (EE) is known to profoundly affect the central nervous system (CNS) at the functional, anatomical and molecular level, both during the critical period and during adulthood. Recent studies focusing on the visual system have shown that these effects are associated with the recruitment of previously unsuspected neural plasticity processes. At early stages of brain development, EE triggers a marked acceleration in the maturation of the visual system, with maternal behaviour acting as a fundamental mediator of the enriched experience in both the foetus and the newborn. In adult brain, EE enhances plasticity in the cerebral cortex, allowing the recovery of visual functions in amblyopic animals. The molecular substrate of the effects of EE on brain plasticity is multi-factorial, with reduced intracerebral inhibition, enhanced neurotrophin expression and epigenetic changes at the level of chromatin structure. These findings shed new light on the potential of EE as a non-invasive strategy to ameliorate deficits in the development of the CNS and to treat neurological disorders.
A Rare Cause of Short Stature: 3M Syndrome in a Patient with Novel Mutation in OBSL1 Gene

The Miller-McKusick-Malvaux (3M) syndrome is a rare autosomal disorder that can lead to short stature, dysmorphic features, and skeletal abnormalities with normal intelligence. A 16-month-old female patient had been referred to our clinic due to short stature. Case history revealed a birth weight of 1740 grams on the 39th week of gestation, with a birth length of 42 cm and no prior hereditary conditions of clinical significance in her family. On physical examination, her length was 67 cm [-3.6 standard deviation (SD) score], weight 7.2 kg (-2.9 SD score), and head circumference 42 cm (below 3rd percentile). She also had numerous characteristic physical features such as a triangular face, fleshy nose tip, a long philtrum, prominent mouth and lips, pointed chin, lumbar lordosis, and prominent heels. As her growth retardation had a prenatal onset and the physical examination results were suggestive of a characteristic profile, the diagnosis of 3M syndrome was strongly considered. Genetic assessment of the patient revealed a novel homozygous p.T45Nfs*40 mutation in the OBSL1 gene. It is recommended that physicians pay further attention to this condition in the differential diagnosis of children with severe short stature.
Lip and vermilion reconstruction with the facial artery musculomucosal flap.

The lips are a complex laminated structure. When lost through injury or disease, they present a complex reconstructive challenge. The facial artery musculomucosal (FAMM) flap is a composite flap with features similar to those of lip tissue. In this article, the anatomy, dissection, and clinical applications for the use of the FAMM flap in lip and vermilion reconstruction are discussed. A series of 16 FAMM flaps in 13 patients is presented. Seven patients had upper-lip reconstruction and six had lower-lip reconstruction. Superiorly based FAMM flaps were used in eight patients, and eight inferiorly based flaps were performed in five patients. Three patients had bilateral, inferiorly based flaps. In summary, the FAMM flap is a local flap that can be used for lip and vermilion reconstruction. Although not identical to the lip, it has many similar features, which make it an excellent option for lip reconstruction.
The evolution of architectural forms through computer visualisation: muqarnas example

Muqarnas is a three-dimensional form whose visual function is to provide the gradual transition between two levels, two sizes, and or two shapes. It evolved over a period of eight centuries and, later, was neglected. Nowadays, it is being copied and introduced into the architecture of the Islamic world, but only as a rigid copy and not as a living evolving form. A long research on the computerisation of muqarnas over the last two decades aimed at pushing further the evolution of this form into new possibilities.
UniqueID: Decentralized Proof-of-Unique-Human

Bitcoin and Ethereum are novel mechanisms for decentralizing the concept of money and computation. Extending decentralization to the human identity concept, we can think of using blockchain for creating a list of verified human identities with a one-person-one-ID property. UniqueID is a Decentralized Autonomous Organization(DAO) for maintaining human identities such that every physical human entity can have no more that one account. One part of this identity is simply the user’s claim on one of his unique, permanent, and measurable characteristics -biometrics. Blockchain has proved its integrity as a platform for storing and performing computations on such claims. The biggest challenge here is to ensure that the user has submitted his own valid biometric data. Human verifiers can check if there is any inconsistency in other users’ data, by peer-to-peer checks. For preventing bad behavior and centralization in the verification process, UniqueID benefits from novel governance mechanisms to choose verifiers and punish unjust ones. Also, there are incentives for honest verifiers and users by newly generated tokens. We show how the users’ privacy can be preserved by using stateof-the-art cryptographic techniques, and so they can use their identity without any concerns for votings, financial and banking purposes, social media accounts, reputation systems etc.
Multigate-Cell Stacked FET Design for Millimeter-Wave CMOS Power Amplifiers

To increase the voltage handling capability of scaled CMOS-based circuits, series connection (stacking) of transistors has been demonstrated in recently reported mm-wave power amplifiers. This paper discusses the implementation of stacked CMOS circuits employing a compact, multigate layout technique, rather than the conventional series connection of individual transistors. A unit multigate FET is composed of a single transistor with one source and drain and multiple (four) gate connections. Capacitances are implemented in a distributed manner allowing close proximity to the individual gate fingers using metal layers available within the CMOS back-end-of-line (BEOL) stack. The multigate structure is demonstrated to decrease parasitic resistances and capacitances, and has better layout for heat-sinking. The unit cell is replicated through tiling to implement larger effective gate widths. Millimeter-wave power amplifiers using the multigate-cell are presented which operate over the 25-35 GHz band and achieve 300 mW of saturated output power and peak power-added efficiency (PAE) of 30% in 45 nm CMOS SOI technology. To the authors' knowledge, the output power is the best reported for a single stage CMOS power amplifier that does not use power-combining for this frequency range.
Modeling and Control of Marine Diesel Generator System With Active Protection

On-board dc grid systems have been proposed in the marine industry to reduce specific fuel consumption and to improve dynamic performance and manoeuvrability. The primary energy sources of an on-board dc system are variable frequency operating diesel engine generators with an active front-end converter system. Such systems might suffer disturbances from the engine side as well as from the electrical load side. These dynamic conditions result in torque overloads in the mechanical system, resulting in failures to sensitive driveline components. To understand the dynamics associated with disturbances and to propose a robust and reliable system, a detailed modeling approach is required. This paper presents complete modeling of a diesel generator system, including cylinder pressure, mechanical driveline system, electrical generator characteristics, and control system of an active front-end converter. The detailed model is used to develop a novel power electronic-based controller to reduce elevated load levels induced during disturbances. The controller increases the damping ratio of the first natural frequency by using the speed difference between a generator and a flywheel. The generator speed is estimated while fly wheel inertia speed is measured from an existing speed sensor used for monitoring and electronic control, and their difference is used to improve the reliability under disturbance conditions. Simulation with the detailed model has indicated excessive drivetrain loads and potential damage to critical components. The proposed controller enhances the damping of the system by transferring the torsional energy to the electrical system, reducing the shaft torque amplitude during resonance. This paper presents simulation results demonstrating the fidelity of the diesel generator model as well as the effectiveness of the proposed controller.
Cerebellar ataxia rehabilitation trial in degenerative cerebellar diseases.

To investigate short- and long-term effects of intensive rehabilitation on ataxia, gait, and activities of daily living (ADLs) in patients with degenerative cerebellar disease.



A total of 42 patients with pure cerebellar degeneration were randomly assigned to the immediate group or the delayed-entry control group. The immediate group received 2 hours of inpatient physical and occupational therapy, focusing on coordination, balance, and ADLs, on weekdays and 1 hour on weekends for 4 weeks. The control group received the same intervention after a 4-week delay. Short-term outcome was compared between the immediate and control groups. Long-term evaluation was done in both groups at 4, 12, and 24 weeks after the intervention. Outcome measures included the assessment and rating of ataxia, Functional Independence Measure, gait speed, cadence, functional ambulation category, and number of falls.



The immediate group showed significantly greater functional gains in ataxia, gait speed, and ADLs than the control group. Improvement of truncal ataxia was more prominent than limb ataxia. The gains in ataxia and gait were sustained at 12 weeks and 24 weeks, respectively. At least 1 measure was better than at baseline at 24 weeks in 22 patients.



Short-term benefit of intensive rehabilitation was evident in patients with degenerative cerebellar diseases. Although functional status tended to decline to the baseline level within 24 weeks, gains were maintained in more than half of the participants.
Magnetic Resonance for Wireless Power Transfer [A Look Back]

Magnetic resonance has been a cornerstone of nonradiative wireless power transfer (WPT) since the late 19th century. However, some researchers have the misconception that magnetic resonance for WPT was developed recently. This article traces some early work of Tesla and other researchers related to the use of magnetic resonance in WPT. Included are some examples of magnetic resonance-based WPT projects conducted by researchers in the biomedical and power electronics communities over the last few decades. Two principles used in WPT are reiterated in this article, and their advantages and disadvantages are addressed. Some issues that may affect future trends of short- and midrange applications are discussed.
A Beginner's Guide to Interferometric SAR Concepts and Signal Processing [AESS Tutorial IV]

Interferometric synthetic aperture radar (IFSAR, also abbreviated as InSAR) employs pairs of high resolution SAR images to generate high quality terrain elevation maps using phase interferometry methods. IFSAR provides an all-weather, day/night capability to generate measurements of terrain elevation on a dense grid of sample points with accuracies of ones of meters. Both spaceborne and airborne IFSAR systems are in use. In this paper we present a tutorial introduction to the concepts, techniques, and applications of IFSAR. After a brief introduction to digital elevation models (DEMs) and digital terrain elevation data (DTED), the fundamental IFSAR equation relating interferometric phase measurements to terrain elevation is derived from simple geometric considerations. The central section of the paper describes the major algorithmic steps required to form an IFSAR terrain map. Finally, variations of IFSAR for mapping terrain elevation or reflectivity changes are briefly described. A Web site at users.ece.gatech.edu/~mrichard/AESSJFSAR.htm provides access to color versions of many of the IFSAR images included in this paper.
Microenvironmental regulation of tumour angiogenesis

Tumours display considerable variation in the patterning and properties of angiogenic blood vessels, as well as in their responses to anti-angiogenic therapy. Angiogenic programming of neoplastic tissue is a multidimensional process regulated by cancer cells in concert with a variety of tumour-associated stromal cells and their bioactive products, which encompass cytokines and growth factors, the extracellular matrix and secreted microvesicles. In this Review, we discuss the extrinsic regulation of angiogenesis by the tumour microenvironment, highlighting potential vulnerabilities that could be targeted to improve the applicability and reach of anti-angiogenic cancer therapies.
Incomplete Multisource Transfer Learning

Transfer learning is generally exploited to adapt well-established source knowledge for learning tasks in weakly labeled or unlabeled target domain. Nowadays, it is common to see multiple sources available for knowledge transfer, each of which, however, may not include complete classes information of the target domain. Naively merging multiple sources together would lead to inferior results due to the large divergence among multiple sources. In this paper, we attempt to utilize incomplete multiple sources for effective knowledge transfer to facilitate the learning task in target domain. To this end, we propose an incomplete multisource transfer learning through two directional knowledge transfer, i.e., cross-domain transfer from each source to target, and cross-source transfer. In particular, in cross-domain direction, we deploy latent low-rank transfer learning guided by iterative structure learning to transfer knowledge from each single source to target domain. This practice reinforces to compensate for any missing data in each source by the complete target data. While in cross-source direction, unsupervised manifold regularizer and effective multisource alignment are explored to jointly compensate for missing data from one portion of source to another. In this way, both marginal and conditional distribution discrepancy in two directions would be mitigated. Experimental results on standard cross-domain benchmarks and synthetic data sets demonstrate the effectiveness of our proposed model in knowledge transfer from incomplete multiple sources.
Evaluating Dialogs based on Grice’s Maxims

There is no agreed upon standard for the evaluation of conversational dialog systems, which are well-known to be hard to evaluate due to the difficulty in pinning down metrics that will correspond to human judgements and the subjective nature of human judgment itself. We explored the possibility of using Grice’s Maxims to evaluate effective communication in conversation. We collected some system generated dialogs from popular conversational chatbots across the spectrum and conducted a survey to see how the human judgements based on Gricean maxims correlate, and if such human judgments can be used as an effective evaluation metric for conversational dialog.
Automatic detection of diabetic retinopathy exudates from non-dilated retinal images using mathematical morphology methods

Diabetic retinopathy is a complication of diabetes that is caused by changes in the blood vessels of the retina. The symptoms can blur or distort the patient's vision and are a main cause of blindness. Exudates are one of the primary signs of diabetic retinopathy. Detection of exudates by ophthalmologists normally requires pupil dilation using a chemical solution which takes time and affects patients. This paper investigates and proposes a set of optimally adjusted morphological operators to be used for exudate detection on diabetic retinopathy patients' non-dilated pupil and low-contrast images. These automatically detected exudates are validated by comparing with expert ophthalmologists' hand-drawn ground-truths. The results are successful and the sensitivity and specificity for our exudate detection is 80% and 99.5%, respectively.
IUI workshop on interactive machine learning

Many applications of Machine Learning (ML) involve interactions with humans. Humans may provide input to a learning algorithm (in the form of labels, demonstrations, corrections, rankings or evaluations) while observing its outputs (in the form of feedback, predictions or executions). Although humans are an integral part of the learning process, traditional ML systems used in these applications are agnostic to the fact that inputs/outputs are from/for humans.
 However, a growing community of researchers at the intersection of ML and human-computer interaction are making interaction with humans a central part of developing ML systems. These efforts include applying interaction design principles to ML systems, using human-subject testing to evaluate ML systems and inspire new methods, and changing the input and output channels of ML systems to better leverage human capabilities. With this Interactive Machine Learning (IML) workshop at IUI 2013 we aim to bring this community together to share ideas, get up-to-date on recent advances, progress towards a common framework and terminology for the field, and discuss the open questions and challenges of IML.
Analysis of a low-dimensional bottleneck neural network representation of speech for modelling speech dynamics

This paper presents an analysis of a low-dimensional representation of speech for modelling speech dynamics, extracted using bottleneck neural networks. The input to the neural network is a set of spectral feature vectors. We explore the effect of various designs and training of the network, such as varying the size of context in the input layer, size of the bottleneck and other hidden layers, and using input reconstruction or phone posteriors as targets. Experiments are performed on TIMIT. The bottleneck features are employed in a conventional HMMbased phoneme recognition system, with recognition accuracy of 70.6% on the core test achieved using only 9-dimensional features. We also analyse how the bottleneck features fit the assumptions of dynamic models of speech. Specifically, we employ the continuous-state hidden Markov model (CS-HMM), which considers speech as a sequence of dwell and transition regions. We demonstrate that the bottleneck features preserve well the trajectory continuity over time and can provide a suitable representation for CS-HMM.