Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images

MOTIVATION Neutrophil extracellular traps (NETs) are believed to be essential in controlling several bacterial pathogens. Quantification of NETs in vitro is an important tool in studies aiming to clarify the biological and chemical factors contributing to NET production, stabilization and degradation. This estimation can be performed on the basis of fluorescent microscopy images using appropriate labelings. In this context, it is desirable to automate the analysis to eliminate both the tedious process of manual annotation and possible operator-specific biases. RESULTS We propose a framework for the automated determination of NET content, based on visually annotated images which are used to train a supervised machine-learning method. We derive several methods in this framework. The best results are obtained by combining these into a single prediction. The overall Q(2) of the combined method is 93%. By having two experts label part of the image set, we were able to compare the performance of the algorithms to the human interoperator variability. We find that the two operators exhibited a very high correlation on their overall assessment of the NET coverage area in the images (R(2) is 97%), although there were consistent differences in labeling at pixel level (Q(2), which unlike R(2) does not correct for additive and multiplicative biases, was only 89%). AVAILABILITY AND IMPLEMENTATION Open source software (under the MIT license) is available at https://github.com/luispedro/Coelho2015_NetsDetermination for both reproducibility and application to new data.
Calcareous nannoplankton and planktonic foraminifera of the Messinian and basal Pliocène from capo san Marco (W. Sardinia)

Une etude du Nannoplancton calcaire et des Foraminiferes planctoniques provenants du Tortonien superieur, du Messinien et du Pliocene transgressif de la coupe de Capo San Marco (Sardaigne SO) a fourni les resultats suivants : 1. La partie inferieure de cette coupe appartient a la zone NN 11 (zone a Discoaster quinqueramus), respective a la partie superieure de la zone a Globorotalia acostaensis acostaensis et a la partie inferieure de la zone a Globorotalia conomiozea. 2. Le Messinien superieur ne contient pas des faunes planctoniques a cause des conditions ecologiques, provoques par la crise de salinite pendent cette periode. 3. Le Pliocene transgressif appartient a la zone NN 12 (zone a Ceratolithus tricorniculatus), respective a la zone a Globorotalia margaritae.
Fast and Accurate Genome-Wide Association Test of Multiple Quantitative Traits

Multiple correlated traits are often collected in genetic studies. By jointly analyzing multiple traits, we can increase power by aggregating multiple weak effects and reveal additional insights into the genetic architecture of complex human diseases. In this article, we propose a multivariate linear regression-based method to test the joint association of multiple quantitative traits. It is flexible to accommodate any covariates, has very accurate control of type I errors, and offers very competitive performance. We also discuss fast and accurate significance p value computation especially for genome-wide association studies with small-to-medium sample sizes. We demonstrate through extensive numerical studies that the proposed method has competitive performance. Its usefulness is further illustrated with application to genome-wide association analysis of diabetes-related traits in the Atherosclerosis Risk in Communities (ARIC) study. We found some very interesting associations with diabetes traits which have not been reported before. We implemented the proposed methods in a publicly available R package.
Scalable Computing: Practice and Experience

Evolutionary structural testing is a technique that uses specific approaches based on guided searches algorithms. It involves evaluating fitness functions to determine whether test data satisfy or not various structural testing criteria. For testing multi-way decision constructs the nested If-Then-Else structure and Alternative Critical Branches (ACBs) approaches are generally used. In this paper a new evolutionary structural approach based on Compact and Minimized Control Flow Graph (CMCFG) which uses two different formulas for evaluating the performance of test data, is presented. The CMCFG approach is derived from the concept of Control Flow Graph (CFG). Experiments on different Switch-Case constructs with different nesting levels have demonstrated that CMCFG yields significantly better results in finding test data which cover a particular target branch in comparison with the previous approaches.
SpaceBot: Towards Participatory Evaluation of Smart Buildings

Smart buildings generate a wealth of data about the spaces they contain. Yet, in evaluating them against occupant needs, sensor data alone is insufficient. Our contribution lies in a re-framing of smart building spaces around the human factor, and a critical lens on the criteria used to evaluate buildings. We propose future work on participatory technologies to evaluate complex and heterogeneous built environments with the people who live and work in them, recognising that their expertise is invaluable in creating quality spaces and ensuring their ongoing and sustainable use.
Early Medical Skull Surgery for Treatment of Post-Traumatic Osteomyelitis 5,000 Years Ago

Here we describe the findings of a unique example of the early techniques adopted in neurosurgery around 5000 years ago, consisting in a double well healed skull trephination associated with a post-cranial traumatic event occurring intra vitam to a young male from the Early Chalcolithic cemetery of Pontecagnano (South Italy, ca. 4,900 - 4,500 cal BP). Morphological, X-ray and 3D-CT scan skull-cap evaluation revealed that the main orifice was produced by scraping, obtained by clockwise rotary motion of a right-handed surgeon facing the patient, while the partial trephination was carried out by using a stone point as a drilling tool. In both cases, bone regrowth is indicative of the individual's prolonged postoperative survival and his near-complete recovery. The right femur shows a poorly healed mid-shaft fracture presumably induced by a high energy injury, and a resulting chronic osteomyelitis, affecting both femurs by hematogenous spread of the infection. Our observations on the visual and radiological features of skull and femur lesions, along with evidence on the timing of experimental bone regrowth vs. healing of lower limb fractures associated to long-term bone infections now suggest that this young man underwent a double skull trephination in order to alleviate his extremely painful condition induced by chronic osteomyelitis, which is thought to have been the cause of death.
LiDAR Data Classification Using Morphological Profiles and Convolutional Neural Networks

In recent years, deep learning-based methods, especially convolutional neural networks (CNNs), have shown their capabilities in remote sensing data processing. The efficacy of light detection and ranging (LiDAR) has been already proven in a wide variety of research areas. Most of the existing methods do not extract the informative features from LiDAR-derived rasterized digital surface models (LiDAR-DSM) data in a deep manner. In order to utilize the advantages of deep models for the classification of LiDAR-derived features, deep CNN is proposed here to hierarchically extract the robust and discriminant features of the input data. Moreover, morphological profiles and multiattribute profiles (MAPs) are investigated to enrich the inputs of the CNN and further to improve the ultimate classification performance. Furthermore, a new activation function, sigmoid-weighted linear units (SiLUs), is introduced. The proposed frameworks are tested on two LiDAR-DSMs (i.e., Bayview Park and Houston data sets). The MAP-CNNs with SiLU outperform original CNNs by 6.62% and 6.88% in terms of overall accuracy on Bayview Park and Houston data sets, respectively, when the number of training samples of each class is 40.
Effects of Tibetan Music on Neuroendocrine and Autonomic Functions in Patients Waiting for Surgery: A Randomized, Controlled Study

Background The aim of this study was to investigate the effects of listening to Tibetan music on anxiety and endocrine, autonomic, cognitive responses in patients waiting for urologic surgery. Methods Sixty patients waiting for surgery were enrolled to the study. They were randomized in music (M) and control (C) groups. The M group listened to a low-frequency Tibetan music for 30 min (T0–T30) through headphones, and the C group wore headphones with no sound. The State Trait Anxiety Inventory Questionnaire (STAI) Y-1 was administered at T0 and T30. Normalized low (LFnu) and high frequencies (HFnu) of heart rate variability, LF/HF ratio, and galvanic skin response (GRS) data were analyzed at T0, T10, T20, T30, and T35. The salivary α-amylase (sAA) samples were collected at T0, T35, and T45. Results In the M group, the STAI Y-1 score decreased at T30 versus baseline (p < 0.001), sAA levels decreased at T35 versus T0(p=0.004), and GSR remained unchanged. In the C group, the STAI Y-1 score remained unchanged, sAA level increased at T35 versus T0(p < 0.001), and GSR slightly increased at T35 versus baseline (p=0.359). LFnu was lower, and HFnu was significantly higher (T10–T30) in M versus C group. Mean LF/HF ratio slightly reduced in the M group. Conclusions Our results suggest that preoperative listening to relaxing Tibetan music might be a useful strategy to manage preoperative anxiety.
A method for estimating process maliciousness with Seq2Seq model

In recent years, cyber-attacks become more sophisticated and the damage caused by these attacks also becomes serious problem. In these attacks, specially-crafted malware, which utilizes countermeasures such as post execution binary elimination or process injection, is used not to be noticed by a target. Therefore, it is hard to detect malware used in these attacks with binary-dependent method before the intrusion, and the countermeasure after intrusion is required. This paper proposes an infection detection method by estimating maliciousness of processes in Windows machines. In our proposal, we extract feature vector sequence from process behavior captured by Process Monitor with Seq2Seq model at first, and then estimate the process maliciousness by classifying with the other Seq2Seq model. We evaluated the performance of our proposal by 5-fold cross validation and compared the performance with the method using uni-gram feature.
A recommendation algorithm for collaborative denoising auto-encoders based on user preference diffusion

The main challenge of collaborative filtering is to use a relatively less effective score to get an accurate prediction. It is an effective method to incorporate user and item information with collaborative filtering. In this paper, we present a new method. Firstly, the heterogeneous information network is used to combine more information of users and items. Under the corresponding user interest semantic assumptions, the observed user implicit feedback extends the user's preference items along different meta-paths. And then combined with the Collaborative Denoising Auto-Encoder (CDAE) for top-N recommendation. Denoising Auto-Encoders learns latent representation of corrupted user-item preferences that can best reconstruct the full input. Experiments show that the proposed algorithm can effectively alleviate the sparse data and improve the performance in terms of recommendation accuracy.
Wtap is required for differentiation of endoderm and mesoderm in the mouse embryo

Wilms' tumor 1‐associating protein (WTAP) was previously identified as a protein associated with Wilms' tumor‐1 (WT‐1) protein that is essential for the development of the genitourinary system. Although WTAP has been suggested to function in alternative splicing, stabilization of mRNA, and cell growth, its in vivo function is still unclear. We generated Wtap mutant mice using a novel gene‐trap approach and showed that Wtap mutant embryos exhibited defective egg‐cylinder formation at the gastrulation stage and died by embryonic day 10.5. Although they could form extraembryonic tissues and anterior visceral endoderm, Wtap mutant embryos and embryonic stem cells failed to differentiate into endoderm and mesoderm. The chimera analysis showed that Wtap in extraembryonic tissues was required for the formation of mesoderm and endoderm in embryonic tissues. Taken together, our findings indicate that Wtap is indispensable for differentiation of mesoderm and endoderm in the mouse embryo. Developmental Dynamics 237:618–629, 2008. © 2008 Wiley‐Liss, Inc.
HVSM: Hardware-variability aware streaming processors' management policy in GPUs

GPUs are widely used in general-purpose high performance computing field due to their highly parallel architecture. In recent years, a new era with nanometer scale integrated circuit manufacture process has come, as a consequence, GPUs' computation capability gets even stronger. However, as process technology scales down, hardware variability, e.g., process variations (PVs) and negative bias temperature instability (NBTI), has a higher impact on the chip quality. The parallelism of GPU desires high consistency of hardware units on chip, otherwise, the worst unit will inevitably become the bottleneck. So the hardware variability becomes a pressing concern to further improve GPUs' performance and lifetime, not only in integrated circuit fabrication, but more in GPU architecture design. Streaming Processors (SPs) are the key units in GPUs, which perform most of parallel computing operations. Therefore, in this work, we focus on mitigating the impact of hardware variability in GPU SPs. We first model and analyze SPs' performance variations under hardware variability. Then, we observe that both PV and NBTI have large impact on SP's performance. We further observe unbalanced SP utilization, e.g., some SPs are idle when others are active, during program execution. Leveraging both observations, we propose a Hardware Variability-aware SPs' Management policy (HVSM), which dynamically prioritizes the fast SPs, regroups SPs in a two-level granularity and dispatches computation in appropriate SPs. Our experimental results show HVSM effectively reduces the impact of hardware variability, which can translate to 28% performance improvement or 14.4% lifetime extension for a GPU chip.
Micro-structural evolution in plastically deformed crystalline materials

(07/11/2019) Micro-structural evolution in plastically deformed crystalline materials Two rate-independent strain gradient crystal plasticity models are developed and applied in numerical studies designed to identify the properties inherent to model predictions of plastic deformation. The two models incorporate gradients of slip into the framework of conventional crystal plasticity in order to model size-dependent plasticity effects. This gradient dependence is achieved by relating a slip measure which combines both slip and their gradients to a shear hardening curve, as commonly done in conventional plasticity theories. Finite element codes are implemented which allow for numerical predictions for the two models to be obtained. Application of the two models to the pure shear boundary value problem is used to characterize plastic behavior, which also allows for the identification of inherent properties through closed form expressions. Single crystal Monazite containing a void is studied through a plane analysis. The conditions that allow for a plane analysis of single crystal Monazite are identified through crystallographic symmetry considerations. Predictions of the slip and micro-structure around a void are presented for size-independent and size-dependent plastic behavior, highlighting the effects due to gradients of slip.
Developing a Valid and Reliable Instrument to Predict the Protective Sexual Behaviors in Women at Risk of Human Immunodeficiency Virus

Background: One much needed tool to assist with the monitoring and evaluation of Human Immunodeficiency Virus (HIV) prevention programs is to provide a valid instrument to measure protective sexual behavior and related factors. Objectives: The current study aimed to design a valid and reliable instrument to predict the protective sexual behaviors of women at risk of HIV in Iran. Patients and Methods: The current study was a sequential mixed cross-sectional and methodological research. Initially, via a qualitative research, constructs and factors associated with sexual protective behavior of women at risk were identified through 25 in-depth interviews. The questionnaire on predictors of protective sexual behaviors in women at risk of HIV (PSPB) was designed based on a qualitative study, and then its qualitative validity, content, and construct validity were evaluated. Exploratory factor analysis was performed and 200 women at risk participated. Results: Seven concepts emerged after exploratory factor analysis of the 48 items. The content validity ratio (CVR) of the questionnaire constructs were 0.55 to 0.76, and content validity index (CVI) structure was 0.86 to 0.95. Cronbach's alpha coefficient for the entire questionnaire was 0.78, and correlation coefficient of the test-retest reliability for the constructs was from 0.73 to 0.89. Conclusions: The current study proved the capability of the predictors of sexual protective behavior in women at risk for HIV questionnaire as a valid and reliable instrument for the Iranian community.
Cooperative spectrum occupancy measurements in the 2.4 GHz ISM band

This paper presents cooperative spectrum occupancy measurements in the 2.4 GHz ISM band. Spectrum occupancy describes the efficiency of spectrum use in terms of the proportion of time that the bands are occupied. In this paper, spectrum occupancy is measured from two measurement devices with several directional antennas. The spectrum occupancy information obtained from the different antennas and measurement devices is combined using techniques known from the cooperative spectrum sensing research for future cognitive radio systems. We introduce a new metric, the cooperative spectrum occupancy, to characterize the resulting spectrum occupancy that is obtained by combining the occupancy measurements from the antennas with different combining techniques, such as AND, OR, and majority combining rules. Since the transmission power levels at ISM band are low to allow efficient frequency reuse, the resulting spectrum occupancies are heavily dependent on the measurement location. Instead of averaging out the influence of the spatial dimension, the new metric can give more insights into the actual spectrum occupancy in a given area taking into account the spatial dimension.
Semantic Parsing via l_{0}-norm-based Alignment

In this paper, we explore the IBM Model with a ‘0-norm prior to the semantic parsing which parses a sentence to its corresponding meaning representation, and compare two supervised probabilistic Combinatory Categorial Grammar (PCCG) online learning approaches that are Unification-Based Learning (UBL) method and Factored Unification-Based Learning (FUBL) one. Specially, we extend manually GeoQuery and ATIS datasets from English to Chinese pinyinformat string. The experiment on such benchmark datasets in both English and Chinese with two different meaning representations (i.e., lambda-calculus and variable-free expressions) demonstrates that both methods adopted this IBM Model with ‘0-norm outperform trivially those that used the IBM Model without‘0norm, and also shows small improvements of around 0.1% 0.7% of F1 for the two algorithms on nearly all conditions.
A new Wi-Fi fingerprint indoor localisation method for smart phone's heterogeneity

Wi-Fi fingerprint indoor localisation method is widely used owing to its low cost and relatively high accuracy. However, a primary problem for fingerprinting is that different devices receive different signal strength even at the same time and in the same place, thus affecting the localisation accuracy extremely. We propose a new method which makes use of RSS histogram generated by radio map and real-time RSS sequence respectively to form a linear relationship between reference devices and users’ devices. Therefore, once an observed RSS is received, it is transformed to a new fingerprint to fit the radio map. Our experiments use two different devices to verify the RSS-calibration method’s performance compared with that of no calibration and manual calibration. And it indicates that the localisation accuracy is improved by about 2 m.
Underutilisation of self-service libraries in Chinese cities: The absence of a patron-centric perspective

Purpose Self-service libraries (SSLs) have been regarded as an effective approach to provide convenient book services to the enormously large populations of China’s cities. These SSLs are in fact automatic book service machines, which provide a combination of services, including reading card issuing, book lending and returning, and book reservations and collection. However, despite acclaimed success, SSL services are not well received by patrons and are underutilised. The purpose of this paper is to identify and understand the causes of the underutilisation of SSL services in Chinese cities. Design/methodology/approach This study adopted an inductive approach and a case study research design. The SSL services in Wuhan, the capital city of Hubei Province, were adopted as the case study, in which 20 public librarians, SSL workers and managers, and library patrons were approached and interviewed using semi-structured question scripts. The interview data were analysed using a thematic analysis approach. Findings The analysis pointed to 13 causes in three main themes: management problems, service limitations, and the implicit role of government. Further conceptualisation of the findings revealed that the underutilisation of SSL services has resulted from the absence of a patron-centric perspective and the negligence of patrons’ needs and requirements. Therefore, to increase the popularity and usage of SSLs, it is necessary to develop patron-centric management mechanisms through which patrons’ needs and requirements can be effectively understood and responded to. Originality/value This study aims to develop specific suggestions to improve the usage of SSLs. Furthermore, although this study focuses on SSL development in China, this research can provide useful suggestions and implications that can be shared across international borders.
Probing the viability of TCP extensions

TCP was designed with extendibility in mind, chiefly reflected in the options mechanism. However, there have been repeated observations of misbehaving middleware that have hampered the deployment of beneficial TCP extensions. This paper reports on an experiment to determine how prevalent three types of behaviour are. We find that 9.08% of hosts don’t respond to SYN frames with payloads, 0.17% of hosts don’t respond to SYN frames with non-standard options and 0.56% of hosts don’t respond to SYN frames which attempt to negotiate ECN.
On the splitting method for vector quantization codebook generation

The well-known LBG algorithm uses binary splitting for gen- erating an initial codebook, which is then iteratively improved by the generalized Lloyd algorithm (GLA). We study different variants of the splitting method and its application to codebook generation with and without the GLA. A new iterative splitting method is proposed, which is applicable to codebook generation without the GLA. Experiments show that the improved splitting method outperforms both the GLA and the other existing splitting-based algorithms. The best combination uses hy- perplane partitioning of the clusters along the principal axis as proposed by Wu and Zhang, integrated with a local repartitioning phase at each step of the algorithm. © 1997 Society of Photo-Optical Instrumentation Engineers. (S0091-3286(97)02311-8)