Miracle-dz/UniFAR-FTUs huggingface dataset:
Supplementary material for : How transferable are features in deep neural networks ?

Since Krizhevsky et al. (2012) won the ImageNet 2012 competition, there has naturally been much interest and work toward tweaking hyperparameters of large convolutional models. For example, Zeiler and Fergus (2013) found that it is better to decrease the first layer filters sizes from 11 × 11 to 7 × 7 and to use a smaller stride of 2 instead of 4. However, because this study aims not for maximum absolute performance but to use a commonly studied architecture, we used the reference implementation provided by Caffe (Jia et al., 2014). We followed Donahue et al. (2013) in making a few minor departures from Krizhevsky et al. (2012) when training the convnets in this study. We skipped the data augmentation trick of adding random multiples of principle components of pixel RGB values, which produced only a 1% improvement in the original paper, and instead of scaling to keep the aspect ratio and then cropping, we warped images to 256× 256. We also placed the Local Response Normalization layers just after the pooling layers, instead of before them. As in previous studies, including Krizhevsky et al. (2012), we use dropout (Hinton et al., 2012) on fully connected layers except for the softmax output layer.
Selective potentiation of gynecologic cancer cell growth in vitro by electromagnetic fields.

OBJECTIVE Epidemiological data suggest that exposure to electromagnetic fields (EMF) may increase the risk of various cancers. We evaluated EMF effects on the in vitro growth response of human cell lines isolated from various reproductive tract tissues. We also assessed the effects of EMF on cisplatin- or paclitaxel-induced cytotoxicity. METHODS Endometrial, ovarian, and prostate cancer cell lines as well as immortalized endometrial stromal cells and immortalized ovarian epithelial cells were exposed continually to EMF. Proliferation was assessed by the metabolic activity assay, MTT, direct cell counting, and anchorage-independent colony formation in soft agar. Cytotoxicity induced by cisplatin or paclitaxel was assessed using the MTT assay. RESULTS Continuous exposure to EMF at field strengths of 2 G enhanced proliferation of two human prostate and three endometrial, but only one ovarian, cancer cell lines. EMF enhanced metabolic activity of cancer cells within 96 h and increased absolute cell number (anchorage-dependent proliferation) and colony-forming efficiency (anchorage-independent proliferation) over sham-treated controls. EMF had no effect on cytotoxicity induced by the chemotherapeutic agents Taxol or cisplatin. CONCLUSIONS Continuous exposure to EMF can enhance growth rates of transformed cells for some human epithelial cancers. Cancer cells from the steroid sex hormone regulated tissues of endometrium and prostate appeared to be more responsive to EMF than cells from ovarian cancers.
Identifying nearby field T dwarfs in the UKIDSS Galactic Clusters Survey

We present the discovery of two new late-T dwarfs identified in the UKIRT Infrared Deep Sky Survey (UKIDSS) Galactic Clusters Survey (GCS) Data Release 2 (DR2). These T dwarfs are nearby old T dwarfs along the line of sight to star-forming regions and open clusters targeted by the UKIDSS GCS. They are found towards thePer cluster and Orion complex,respectively, from a search in 54 square degrees surveyed in five filters. Photometric candidates were picked up in two-colour diagrams, in a very similar manner to candidates extracted from the UKIDSS Large Area Survey (LAS) but taking advantage of the Z filter employed by the GCS. Both candidates exhibit near-infrared J-band spectra with strong methane and water absorption bands characteristic of late-T dwarfs. We derive spectral types of T6.5±0.5 and T7±1 and estimate photometric distances less than 50 pc for UGCS J030013.86+490142.5 and UGCS J053022.52 052447.4, respectively. The space density of T dwarfs found in the GCS seems consistent with discoveries in the larger areal coverage of the UKIDSS Large Area Survey, indicating one T dwarf in 6-11 square degrees. The final area surveyed by the GCS, 1000 square degrees in five passbands, will allow expansion of the LAS search area by 25%, increase the probability of finding ultracool brown dwarfs, and provide optimal estimates of contamination by old field brown dwarfs in deep surveys to identify such objects in open clusters and star-forming regions.
Comparison of GonoGen, GonoGen II, and MicroTrak direct fluorescent-antibody test with carbohydrate fermentation for confirmation of culture isolates of Neisseria gonorrhoeae

When testing 248 clinical isolates of Neisseria gonorrhoeae, the sensitivity was 100% with GonoGen (Becton Dickinson Microbiology Systems), 99.6% (247 of 248) with GonoGen II (Becton Dickinson), 97.2% (241 of 248) with the MicroTrak direct fluorescent-antibody test (Syva), and 97.6% (242 of 248) with Rapid Fermentation Agar carbohydrates (Remel). Of 62 isolates of other Neisseria species, none was misidentified as N. gonorrhoeae by GonoGen, MicroTrak, or Rapid Fermentation Agar carbohydrates but 7 (31.8%) of 22 isolates of N. meningitidis gave strong, repeatedly false-positive results with GonoGen II. The sensitivity of all four assays was good to excellent, but all positive GonoGen II results should be confirmed with an independent assay, especially when isolates are recovered from sites where N. meningitidis is likely. Positive results from any of the assays should be routinely confirmed when dictated by specific clinical, legal, or microbiological circumstances.
Complete mitochondrial DNA sequence of the endemic Japanese pond turtle Mauremys japonica (Reptilia: Testudines)

Abstract The complete mitochondrial genome of the Japanese pond turtle Mauremys japonica from Japan was analyzed using next-generation sequencing. The mitochondrial genome of M. japonica was identified as a 16,443 bp circular molecule containing 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes, along with 1 A + T-rich control region; the average AT content was 62.82%. One extra base was present at the 174th position in the ND3 gene. The phylogenetic analyses of the complete mitochondrial DNA genes strongly supported the result obtained from the phylogenetic analysis of partial DNA sequences, grouping the monophyletic species within the genus Mauremys.
A comparison of equivolume, equiosmolar solutions of hypertonic saline and mannitol for brain relaxation during elective supratentorial craniotomy

Abstract Background: Hyperosmolar solutions have been used in neurosurgery to reduce brain volume and facilitate surgical exposure. The purpose of this study was to compare the effects of equivolume, equiosmolar solutions of mannitol and hypertonic saline (HS) on brain relaxation, intensive care unit (ICU) and hospital stay, postoperative outcomes and incidence of side-effects in patients undergoing elective supratentorial craniotomy. Methods: In a randomised, prospective, double-blind study, 60 patients undergoing elective supratentorial craniotomy were randomised 1:1 to receive 3 ml/kg of either 20% mannitol or 3% HS. The primary outcome was the surgical condition of the brain assessed by the neurosurgeon using a 4-point scale after opening the dura (1 = relaxed, 2 = satisfactory, 3 = firm and 4 = bulging). Secondary outcomes were electrolytes, blood gases, plasma osmolality and haemodynamic variables measured at 0 min, 30 min, 2 h and 6 h after infusion. Also, predefined postoperative complications, length of ICU and hospital stay were recorded. Appropriate statistical tests were used for comparison; p < 0.05 was considered significant. Results: There was no difference in brain relaxation [mannitol, 1(1–3) versus HS, 1(1.4) points; p = 0.55]. Patients with brain midline shift showed a worse response to hyperosmolar solutions than those without midline shift: 37% versus 8%, respectively; OR = 6.6 (95% CI, 1.54–28.83); p = 0.006. Plasma osmolality increased during the study period (6 h) in both the groups (p < 0.05 compared with baseline). No significant differences in postoperative complications or length of ICU and hospital stay were observed between the groups. Conclusions: Single doses of 3 ml/kg of 20% mannitol and 3% HS are safe and effective for intraoperative brain debulking during elective supratentorial craniotomy, but less effective in patients with pre-existing mass effect and midline shift.
Why people remain inactive during a crisis: Interpreting and dealing with a crisis within a broader social context

Public inactivity has been addressed by scholars across different academic disciplines. Risk communication and behaviour change is difficult and costly due to limited attention to various messages in the public sphere. Crises pose particular challenges if organisations are to communicate effectively with the public to protect them from potential risks. The present study attempts to better understand what makes the public inactive when faced with a crisis. Specifically, I focus on how people perceive a crisis and the reasons they remain inactive during the crisis. Using 28 in-depth interviews with Korean citizens during two food-related crises, this study revealed that people interpreted the crisis within a broader social context, made underlying assumptions in understanding the crisis and believed what the media vividly showed. The findings also showed that people remained inactive because they avoided dealing with risks due to being distracted by their daily lives, they trusted social systems to manage the problem, and they felt they had high efficacy in resolving the crisis although they did not expect to make fundamental changes in the long-run.
A Deep Learning Approach to Block-based Compressed Sensing of Images

Compressed sensing (CS) is a signal processing framework for efficiently reconstructing a signal from a small number of measurements, obtained by linear projections of the signal. Block-based CS is a lightweight CS approach that is mostly suitable for processing very high-dimensional images and videos: it operates on local patches, employs a low-complexity reconstruction operator and requires significantly less memory to store the sensing matrix. In this paper we present a deep learning approach for block-based CS, in which a fully-connected network performs both the block-based linear sensing and non-linear reconstruction stages. During the training phase, the sensing matrix and the non-linear reconstruction operator are \emph{jointly} optimized, and the proposed approach outperforms state-of-the-art both in terms of reconstruction quality and computation time. For example, at a 25% sensing rate the average PSNR advantage is 0.77dB and computation time is over 200-times faster.
Security aware content-based publish/subscribe system

Improving information propagation in wide-are communication is an important concern of publish/subscribe systems especially for content-based systems. In secure domain, the dissemination of events in a large scale decreases the importance of the event. The issue of confidentiality appears when the plaintexts of events should be kept private from the infrastructure to counter against eavesdropping. Thus, the infrastructure must remain able to make correct routing decisions efficiently. Our goal is to ensure event delivery to consumers in case of malicious dispatchers without decreasing CBPS (content-based publish/subscribe) performances such as expressivity and scalability. This solution is based on smart cards as trusted devices. It uses certificate to enforce security during authentication stage. It is a generic solution applicable for all CBPS.
Association of single nucleotide polymorphisms in the ANKRA2 and CD180 genes with bovine respiratory disease and presence of Mycobacterium avium subsp. paratuberculosis(1).

The objective was to determine whether single nucleotide polymorphisms (SNPs) in the ANKRA2 and CD180 genes are associated with incidence of bovine respiratory disease (BRD) and presence of Mycobacterium avium subsp. paratuberculosis (MAP) in cattle. Two independent populations were used. The first population (BRD-affected; N = 90) was composed of 31 half-sib progeny, from a Brahman × Angus sire, that were treated for BRD. Untreated offspring from the sire were selected to serve as controls. The second population (MAP-infected) of 330 animals of unknown parentage was evaluated for the presence of MAP in ileocecal lymph node and classified as positive or negative. Markers in both genes were assessed for association in these two populations. In the BRD-affected population, five SNPs in the ANKRA2 gene were significantly associated (P < 0.05), and two SNPs were highly associated (P < 0.01) with incidence of BRD. In addition, two SNPs in the CD180 gene were found to be associated with this trait. In the MAP-infected population, one SNP in the ANKRA2 gene was significantly associated (P < 0.05) with the presence or absence of MAP, and a SNP in the CD180 gene was highly associated (P < 0.01) with the trait. Haplotypes, using significant markers, showed a positive association with both incidence of BRD (P = 0.0001) and with the presence of MAP (P = 0.0032). Markers in the ANKRA2 and CD180 genes are associated with the ability of the animal to cope with pathogens.
Coexistence of Fibromuscular Dysplasia and Cystic Medial Necrosis in a Patient With Marfan's Syndrome and Bilateral Carotid Artery Dissections

Background A primary arteriopathy is suspected in most patients with spontaneous dissections of the carotid artery, although the nature of this arteriopathy usually remains elusive. Angiographic changes of fibromuscular dysplasia (FMD), however, are found in 10% to 20% of patients with carotid dissections. Case Description A 26-year-old woman with Marfan's syndrome presented with bilateral amaurosis fugax after surgical repair of an aortic dissection. Angiography revealed a dissection extending from the ascending aorta into the right internal carotid artery and, separate from the aortic dissection, a dissection of the left internal carotid artery. After surgery, microscopic examination of the right carotid artery revealed a medial dissection but no evidence of an underlying arteriopathy, while the left internal carotid artery displayed the typical features of FMD. Eighteen months later the patient died after resection of a large thoracoabdominal aortic dissecting aneurysm. Microscopic examination of the aorta revealed moderately extensive cystic medial necrosis. Conclusions Carotid dissections associated with Marfan's syndrome may be the result of an extension of an aortic dissection or occur isolated from the aorta, even in the same patient. The occurrence of FMD in a patient with Marfan's syndrome in conjunction with previous reports of FMD in a variety of connective tissue disorders suggests that FMD, like cystic medial necrosis, may be a nonspecific disease entity.
Quantitative analysis of static strain sensitivity in human mechanoreceptors from hairy skin.

1. Microelectrode recordings from 15 slowly adapting (SA) cutaneous mechanoreceptor afferents originating in hairy skin were obtained from the radial nerve in humans. 2. Controlled skin stretch was applied to the back of the hand that encompassed the physiological range of skin stretch during movements at the metacarpophalangeal (MCP) joints. 3. Both SA Group I and II afferents showed exquisite dynamic and static sensitivity to skin stretch. The median static strain sensitivity was 1.0 imp.s-1 per percent skin stretch for SAI units and 1.8 for SAII units. 4. Translated into sensitivity to movements at the MCP joint, both SAI and SAII afferents in the skin of the back of the hand displayed a positional sensitivity that was comparable with that reported for muscle spindle afferents. 5. These data give quantitative support to suggestions that skin receptors in the human hairy skin provide information on nearby joint configurations and therefore may play a specific role in proprioception, kinesthesia, and motor control.
Continuous Query Optimization and Evaluation over Unified Linked Stream Data and Linked Open Data Continuous Query Optimization and Evaluation over Unified Linked Stream Data and Linked Open Data

In this report we address the problem of scalable query processing over Linked Stream Data integrated with Linked Open Data. Linked Stream Data consists of data generated by stream sources, e.g., sensors, enriched with semantic descriptions, following the standards proposed for Linked Data. This will enable the easy integration of sensor data with the quickly growing amount of Linked Open Data and facilitate the use of the large body of existing software along with a wide range of novel applications. However, the highly dynamic nature of sensor data requires new approaches for data management and processing which are not supported by existing systems. To remedy this, we present our Continuous Query Evaluation over Linked Streams (CQELS) approach which provides a scalable query processing model for unified Linked Stream Data and Linked Open Data. Scalability in CQELS is achieved by applying state-of-the-art techniques for efficient data storage and query pre-processing, combined with a new adaptive cost-based query optimization algorithm for dynamic data sources, such as sensor streams. In traditional Database Management Systems (DBMS), query optimizers use pre-computed selectivity values for the data to decide on the best execution plan, whereas with continuous query over stream data the data – and consequently its selectivity values – varies over time. This means that the optimal execution plan itself can vary throughout the execution of the query. To overcome this problem, the CQELS query optimizer retains a subset of the possible execution plans and, at query time, updates their respective costs and chooses the least expensive one for executing the query at this given point in time. We have implemented CQELS and our experimental results show that CQELS can greatly reduce query response times while scaling to a realistically high number of parallel queries.
A Review of Towered Big-Data Service Model for Biomedical Text-Mining Databases

The rapid growth of biomedical informatics has drawn increasing popularity and attention. The reason behind this are the advances in genomic, new molecular, biomedical approaches and various applications like protein identification, patient medical records, genome sequencing, medical imaging and a huge set of biomedical research data are being generated day to day. The increase of biomedical data consists of both structured and unstructured data. Subsequently, in a traditional database system (structured data), managing and extracting useful information from unstructured-biomedical data is a tedious job. Hence, mechanisms, tools, processes, and methods are necessary to apply on unstructured biomedical data (text) to get the useful business data. The fast development of these accumulations makes it progressively troublesome for people to get to the required information in an advantageous and viable way. Text mining can help us mine information and knowledge from a mountain of text, and is now widely applied in biomedical research. Text mining is not a new technology, but it has recently received spotlight attention due to the emergence of Big Data. The applications of text mining are diverse and span to multiple disciplines, ranging from biomedicine to legal, business intelligence and security. In this survey paper, the researcher identifies and discusses biomedical data (text) mining issues, and recommends a possible technique to cope with possible future growth.
Indigenous Georgian Wine-Associated Yeasts and Grape Cultivars to Edit the Wine Quality in a Precision Oenology Perspective

In Georgia, one of the most ancient vine-growing environment, the homemade production of wine is still very popular in every rural family and spontaneous fermentation of must, without addition of chemical preservatives, is the norm. The present work investigated the yeast biodiversity in five Georgian areas (Guria, Imereti, Kakheti, Kartli, Ratcha-Lechkhumi) sampling grapes and wines from 22 different native cultivars, in 26 vineyards and 19 family cellars. One hundred and eighty-two isolates were ascribed to 15 different species by PCR-ITS and RFLP, and partial sequencing of D1/D2 domain 26S rDNA gene. Metschnikowia pulcherrima (F’ = 0.56, I’ = 0.32), Hanseniaspora guilliermondii (F’ = 0.49, I’ = 0.27), and Cryptococcus flavescens (F’ = 0.31, I’ = 0.11) were the dominant yeasts found on grapes, whereas Saccharomyces cerevisiae showed the highest prevalence into wine samples. Seventy four isolates with fermentative potential were screened for oenological traits such as ethanol production, resistance to SO2, and acetic acid, glycerol and H2S production. Three yeast strains (Kluyveromyces marxianus UMY207, S. cerevisiae UMY255, Torulaspora delbrueckii UMY196) were selected and separately inoculated in vinifications experiments at a Georgian cellar. Musts were prepared from healthy grapes of local varieties, Goruli Mtsvane (white berry cultivar) and Saperavi (black berry cultivar). Physical (°Brix) and microbial analyses (plate counts) were performed to monitor the fermentative process. The isolation of indigenous S. cerevisiae yeasts beyond the inoculated strains indicated that a co-presence occurred during the vinification tests. Results from quantitative GC-FID analysis of volatile compounds revealed that the highest amount of fermentation flavors, such as 4-ethoxy-4-oxobutanoic acid (monoethyl succinate), 2-methylpropan-1-ol, ethyl 2-hydroxypropanoate, and 2-phenylethanol, were significantly more produced in fermentation conducted in Saperavi variety inoculated with K. marxianus, whereas other aromatic compounds like 3-methylbutyl acetate, ethyl hexanoate and dihydrofuran-2(3H)-one (γ- butyrolactone) showed a higher content in Goruli Mtsvane variety samples fermented by S. cerevisiae. The selected yeast strains have proved to be promising for enhancing the flavor potential in low aromatic Georgian cultivars. This work intends to be a knowledge contribution for a precision oenology toward the strategic concept of “one grape variety-one yeast”.
Distributed dual averaging for convex optimization under communication delays

In this paper we extend and analyze the distributed dual averaging algorithm [1] to handle communication delays and general stochastic consensus protocols. Assuming each network link experiences some fixed bounded delay, we show that distributed dual averaging converges and the error decays at a rate O(T-0.5) where T is the number of iterations. This bound is an improvement over [1] by a logarithmic factor in T for networks of fixed size. Finally, we extend the algorithm to the case of using general non-averaging consensus protocols. We prove that the bias introduced in the optimization can be removed by a simple correction that depends on the stationary distribution of the consensus matrix.