Miracle-dz/UniFAR-FTUs huggingface dataset:
The effectiveness of inking needle core prostate biopsies for preventing patient specimen identification errors: a technique to address Joint Commission patient safety goals in specialty laboratories.

CONTEXT The elimination or reduction of medical errors has been a main focus of health care enterprises in the United States since the year 2000. Elimination of errors in patient and specimen identification is a key component of this focus and is the number one goal in the Joint Commission's 2008 National Patient Safety Goals Laboratory Services Program. OBJECTIVE To evaluate the effectiveness of using permanent inks to maintain specimen identity in sequentially submitted prostate needle biopsies. DESIGN For a 12-month period, a grossing technician stained each prostate core with permanent ink developed for inking of pathology specimens. A different color was used for each patient, with all the prostate cores from all vials for a particular patient inked with the same color. Five colors were used sequentially: green, blue, yellow, orange, and black. The ink was diluted with distilled water to a consistency that allowed application of a thin, uniform coating of ink along the edges of the prostate core. The time required to ink patient specimens comprising different numbers of vials and prostate biopsies was timed. The number and type of inked specimen discrepancies were evaluated. RESULTS The identified discrepancy rate for prostate biopsy patients was 0.13%. The discrepancy rate in terms of total number of prostate blocks was 0.014%. Diluted inks adhered to biopsy contours throughout tissue processing. The tissue showed no untoward reactions to the inks. Inking did not affect staining (histochemical or immunohistochemical) or pathologic evaluation. On average, inking prostate needle biopsies increases grossing time by 20%. CONCLUSIONS Inking of all prostate core biopsies with colored inks, in sequential order, is an aid in maintaining specimen identity. It is a simple and effective method of addressing Joint Commission patient safety goals by maintaining specimen identity during processing of similar types of gross specimens. This technique may be applicable in other specialty laboratories and high-volume laboratories, where many similar tissue specimens are processed.
Cheshire3: retrieving from tera-scale grid-based digital libraries

Recent research in designing and developing digital library services has been focused on approaches to indexing and searching in a steadily increasing range of genres and materials. An important aspect of this research is concerned with providing effective and scalable IR services for digital libraries as these diverse collections grow to sizes measured in terabytes and petabytes. The Cheshire project has had a central research focus on large-scale digital library collections for more than a decade, with a current focus on supporting distributed digital libraries in a Grid evironment. At the same time we have have been prototyping systems for very long term digital preservation, and examining how grid-scale information retrieval systems can interoperate with petabytes of diverse data stored over many years. In order for Information Retrieval (IR) in the evolving “Grid” parallel distributed computing environment[1] to work effectively, there must be a single flexible and extensible series of “Grid Services” with identifiable objects and a known API to handle the IR functions needed for Digital Libraries or other retrieval tasks. The Cheshire3 system builds on the work of the Cheshire project[4] over the past decade to define and implement an easy to use set of IR objects with precisely defined roles that can effectively provide a Grid Service for IR. This demonstration will show how the Cheshire3 system is being applied in distributed information retrieval tasks in large-scale grid-based digital libraries. We will show how the system has been integrated with “Datagrid” services provided by distributed storage systems like the Storage Resource Broker (SRB)[3], and how this enables very large scale storage and retrieval systems with support for data preservation services using the “Multivalent Document” framework[2]. In this demo we will present the results of testing Grid-
Content-fragile watermarking for image authentication

Fragile watermarking addresses the recognition of manipulations. In the moment most fragile watermarks are very sensitive to changes. This is of interest for parties to verify that an image has not been edited, damaged, or altered since it was marked. However in many applications we have to expect several allowed post production editing processes which do not manipulate the content of the image or video data. The semi-fragile schemes address this problem. These techniques are moderately robust and the value identifying the presence of the watermark can serve as a measure of tampering. Unfortunately these schemes cannot recognize if the content or the message of the media was effected or manipulated. Approaches are necessary which can distinguish malicious changes from innocent image processing operations. Such techniques can be termed authentication of the visual content. We propose to extract the visual content, called feature, and embed the content features with a robust watermarking scheme into the image data, called content-fragile watermarking. An integrity decision is based on the extracted feature of the actual image and the embedded watermarking features. Our idea is based on edge characteristics, which are already known and used in several other approaches as content features. To minimize the length of the content feature we introduce and compare five new methods to encode the edge characteristic: two edge shape based feature codes, three statistical feature codes. Our first test results on a selected amount of images show that content fragile watermarking based on robust watermarking and feature extraction allows post production processes and recognizes manipulation.
Synonym, Topic Model and Predicate-Based Query Expansion for Retrieving Clinical Documents

We present a study that developed and tested three query expansion methods for the retrieval of clinical documents. Finding relevant documents in a large clinical data warehouse is a challenging task. To address this issue, first, we implemented a synonym expansion strategy that used a few selected vocabularies. Second, we trained a topic model on a large set of clinical documents, which was then used to identify related terms for query expansion. Third, we obtained related terms from a large predicate database derived from Medline abstracts for query expansion. The three expansion methods were tested on a set of clinical notes. All three methods successfully achieved higher average recalls and average F-measures when compared with the baseline method. The average precisions and precision at 10, however, decreased with all expansions. Amongst the three expansion methods, the topic model-based method performed the best in terms of recall and F-measure.
Theory of coherent time-dependent transport in one-dimensional multiband semiconductor superlattices.

We present an analytical study of one-dimensional semiconductor superlattices in external electric fields, which may be time dependent. A number of general results for the (quasi)energies and eigenstates are derived. An equation of motion for the density matrix is obtained for a two-band model and the properties of the solutions are analyzed. An expression for the current is obtained. Finally, Zener tunneling in a two-band tight-binding model is considered. The present work gives the background and an extension of the theoretical framework underlying our recent Letter [J. Rotvig et al., Phys. Rev. Lett. 74, 1831 (1995)], where a set of numerical simulations was presented.
TECHNOLOGY, TRADE, AND GROWTH: THE ROLE OF EDUCATION

We generalize a trade model with firm-specific heterogeneity and R&D-based growth to allow for endogenous education and fertility. The framework is able to explain cross-country differences in living standards and trade intensities by the differential pace of human capital accumulation among industrialized countries. Consistent with the empirical evidence, scale matters for relative economic prosperity as long as countries are closed, whereas scale does not matter in a fully globalized world. The average human capital of a country, by contrast, influences its relative economic prosperity irrespective of trade-openness.
Role of phosphorylation in conformational adaptability of bovine myelin basic protein

Controlled thrombic digestion of a preparation of components 2 + 3 isolated from the 18.5 kDa bovine myelin basic protein (MBP) yielded a polypeptide that was monophosphorylated on threonine 97 (component 3pT97). This is the first posttranslationally phosphorylated MBP isolated in pure form. We studied the effect of this single phosphate on the conformational adaptability of 18.5 kDa bovine MBP by comparing the circular dichroism (CD) spectrum of component 3pT97 with the spectra of highly purified nonphosphorylated components 1 and 2. The CD spectra of nonphosphorylated component 1 and component 2 [monodeamidated forms(s) of component1] were indistinguishable, while component 3pt97 exhibited a different spectrum. The singly phophorylated MBP component exhibited 13% more ordered conformations than that adopted by nonphosphorylated MBP in dilute aqueous solutions. This was estimated from the CD spectra, and apparently involved about 17 additional amino acid residues in β‐structure(s).
The hydrolysis of penicillin G to 6-amino penicillanic acid by entrapped penicillin acylase.

Penicillin acylase was extracted from Escherichia coli strain ATCC9637, purified and entrapped in celluose triacetate fibres. The enzymewas immobilized by trapping it, as a finely dispersed aqueous phase, in yams of cellulose triacetate by wet spinning. The kinetics of penicillin G hydrolysis were studied by use of several insoluble preparations with different activity content. In an attempt to evaluate the possible industrial applica-tion of the process, the performance of an entrapped acylase reactor was investigated.
Pairwise Linear Discriminant Analysis of Electromyographic signals

Electromyographic (EMG) signals are used as rich information sources for control of intelligent prosthetics. For efficient classification the machine learning algorithms used should allow the nonlinear nature of the multi class problem. For generalized application they should have the analytical ability to systematically tackle the problem in hand. To meet these requirements a pair-wise Linear Discriminant Analysis(LDA) is performed in a systematic manner on EMG signals captured from forehand muscles. A 5 class classification performance from 4 EMG channels are reported along with the ability of the algorithm to scale and visualize complex multidimensional cases.
Medical ontologies to support human disease research and control

In this paper, we discuss an ontology-based system and approach that provides interoperability support for research in and diagnosis of human disease. The proposed solution incorporates a prototype for a Generic Human Disease Ontology (GenDO) that contains common general information regarding human diseases. We adopted the DOGMA formalism for the description and terminology involving ontologies. The proposed GenDO presents the information in four 'dimensions': (a) disease types, (b) causes related to the disease, namely genetic causes (genes, gene complexes and candidate DNA sequence regions) and environmental causes (such as stress, family condition, childhood and age groups), (c) phenotype (observable characteristics of an organism) or symptoms, and (d) treatments available for the disease, such as drug therapy, chemotherapy and physiotherapy. The GenDO also aims to support the study of complex disorders caused simultaneously by many different factors, e.g., the case of psychiatric disorders. We illustrate how this GenDO helps to produce Specific Human Disease Ontologies (SpeDO) upon request, as a support tool for physicians and medical researchers.
Th2 polarization of the immune response of BALB/c mice to Ixodes ricinus instars, importance of several antigens in activation of specific Th2 subpopulations

BALB/c mice were infested with Ixodes ricinus larvae, nymphs or adults. Expression of IL‐4 and IFN‐γ mRNA in axillary and brachial draining lymph node cells were measured by competitive quantitative reverse transcription‐polymerase chain reaction 9 days after the beginning of primary‐infestation. IL‐4 mRNA was always higher than that of IFN‐γ mRNA for all tick instars. Moreover, IL‐4 mRNA expression progressively increased during nymphal primary‐infestation with a high burst of expression 7 days after the beginning of infestation. No evolution of IFN‐γ mRNA expression was detected. Draining lymph node cells of infested BALB/c produced higher level of IL‐4 than IFN‐γ following in vitro restimulation with adult tick saliva, salivary gland extract (SGE) or with five selected different chromatographic fractions of SGE. Anti‐tick IgG1 antibodies but no IgG2a were detected in BALB/c pluri‐infested with I. ricinus nymphs, which confirmed the Th2 polarization of the immune response.
Luminal loop of the ryanodine receptor: a pore-forming segment?

In this issue of the Proceedings, Lynch et al. (1) report a new mutation I4898T in the skeletal muscle Ca2+ release channel/ryanodine receptor (RyR1). The mutation disrupts Ca2+ release channel function, causing severe alterations in muscle structure and function. Ryanodine receptors (RyRs) are Ca2+ channels that control intracellular Ca2+ levels by releasing Ca2+ from the sarco/endoplasmic reticulum (SR), an intracellular Ca2+ storage compartment. Mammalian tissues express three closely related RyR isoforms encoded by separate genes. All three isoforms are found in a variety of tissues, with RyR1 and RyR2 being the primary isoform in skeletal and cardiac muscle, respectively, and RyR3 being found in diaphragm, slow twitch skeletal muscles, and other tissues at low levels (2, 3).
One-year prosthetic outcomes with implant overdentures: a randomized clinical trial.

PURPOSE This randomized clinical trial examined implant overdenture (IOD) fabrication and maintenance time and costs, adjustment and repair incidence, and patient satisfaction after 1 year. MATERIALS AND METHODS Sixty-four patients received 2 mandibular implants and an IOD with either a bar with 2 clips or 2 ball attachments for denture retention. RESULTS Fabrication time, number of appointments, and chair time for adjustments were similar for the 2 denture designs. The most common adjustments for both types were to the IOD contours. Ball-attachment dentures required about 8 times longer for repairs than bar-clip prostheses. Approximately 84% of patients with ball-attachment dentures needed at least 1 repair, versus 20% of those with a bar-clip mechanism. The most common repairs were replacement of the cap spring or cap for the ball-attachment IOD and replacement of a lost or loose clip for bar-clip dentures. DISCUSSION Patients were equally and highly satisfied with the improvements in function, comfort, and appearance with both types of IOD compared to their original conventional dentures. CONCLUSIONS Given equivalent levels of patient satisfaction with either method of retention and a much higher repair rate for the ball attachment, it is suggested that a bar-clip design be used rather than the particular ball attachment utilized in this study.
Face recognition using ensemble support vector machine

In Face recognition, a combination of neural network (NN), known as an ensemble of neural network, often outperforms individual ones. This paper is aiming to present a support vector machines (SVM)-ensemble-based efficient face recognition system. The training samples are randomly chosen by means of bootstrap technique to train the different SVM independently. These SVM's are combined together to generate the ensemble SVM. The proposed method then makes a collective decision by aggregating them. It may be noted that, the performance of the practical SVM is far from the theoretical SVM as the implementations are based on approximated algorithms. The performance of the real SVM can be uplifted by using the proposed ensemble SVM with bagging (bootstrap aggregating). Finally, the proposed method takes the collective decision by aggregating the training samples. The proposed method is validated on AT&T, FERET face databases to show its supremacy over the single SVM-based methods.
Counterexample to an additivity conjecture for output purity of quantum channels

A conjecture arising naturally in the investigation of additivity of classical information capacity of quantum channels states that the maximal purity of outputs from a quantum channel, as measured by the p-norm, should be multiplicative with respect to the tensor product of channels. We disprove this conjecture for p>4.79. The same example (with p=∞) also disproves a conjecture for the multiplicativity of the injective norm of Hilbert space tensor products.
Cell Survival Characteristics and Choline Acetyltransferase Activity in Motor Neurone‐Enriched Cultures from Chick Embryo Spinal Cord

Abstract: The effect of muscle extract on cell survival and choline acetyltransferase (ChAT) activity in cultures of enriched cholinergic neurones from 7‐day chick embryo spinal cord was examined. When neurones were grown on hydrated collagen gels, considerable cell survival and ChAT activity were obtained even in the absence of tissue extract. These parameters were stimulated twofold in the presence of skeletal muscle extract but not liver or skin extracts. The cholinergic neurotrophic activity was found to be heat‐ and trypsin‐sensitive, non‐dialysable, and to act in the virtual absence of glial cells. These data are consistent with a retrogradely acting motor neurone trophic activity.
Syphilitic and Lymphogranuloma Venereum (LGV) Proctocolitis: Clues to a Frequently Missed Diagnosis

A rising incidence of syphilis and lymphogranuloma venereum (LGV) underscores the importance of recognizing these sexually transmitted infections (STI) in routine anocolonic biopsies. To increase awareness of their morphologic manifestations, we undertook a clinicopathologic study of our experience: syphilis (7 patients, 7 specimens), LGV (2 patients, 4 specimens), and syphilis/LGV (1 patient, 3 specimens). The diagnoses of all study specimens were confirmed with pertinent clinical studies. All study patients were human immunodeficiency virus positive, and all 9 with available history were men who have sex with men. The majority presented with bleeding (9), pain (6), and tenesmus (4). Ulcerations were the most common endoscopic abnormality (7), whereas mass lesions were confined to the syphilis group (4). None of the initial impressions included LGV, and syphilis was prospectively suggested only by pathologists (6 of 8) without the knowledge of clinical information and on the basis of morphology. Alternative impressions included condyloma acuminatum (3), inflammatory bowel disease (3), and malignancy (2), among others. All study specimens shared the following histologic core features: an intense lymphohistiocytic infiltrate with prominent plasma cells and lymphoid aggregates, only mild to moderate acute inflammation, minimal basal plasmacytosis and crypt distortion, and only rare granulomas and Paneth cell metaplasia. The spirochetes were focally demonstrated on a Treponema pallidum immunohistochemical stain (1) but not on silver stains (3). All patients with available follow-up data showed resolution of symptoms and imaging abnormalities after STI therapy (6). In summary, we report a unique pattern of STI proctocolitis consistently identified in patients with serologically confirmed syphilis and/or LGV infection; pertinent STI therapy leads to resolution of clinical abnormalities. This histologic pattern is important to recognize for timely treatment, for prevention of onward STI transmission, and to avoid the diagnostic pitfalls of inflammatory bowel disease or malignancy.
Chromosomal Instability, Colorectal Cancer and Taxane Resistance

mitosis. Aberrations in key regulators of this process have been found in humanmalignancies associated with chromosomal instability (CIN). Importantchemotherapeutic agents which alter microtubule dynamics such as paclitaxel andvincristine, prolong spindle checkpoint activation and delay the completion ofmitosis. Intriguingly, inhibition of BubR1 or overexpression of Aurora kinase A,spindle checkpoint regulators implicated in CIN, promote resistance to microtubuleinhibitors (MTIs) in vitro. Taxanes have failed to demonstrate significant clinicalbenefit in phase II trials in colorectal cancer (CRC). The high incidence of CIN in thisdisease, coupled with alterations in spindle checkpoint regulators in vivo, may explainthe disappointing results associated with taxane based therapies for CRC. A phase IItrial of taxanes in patients with metastatic CIN negative CRC may be indicated.
A TOPOLOGICAL DATA ANALYSIS APPROACH TO THE EPIDEMIOLOGY OF INFLUENZA

Influenzanet is a system to monitor the activity of influenza-like-illness [ILI] with the aid of internet volunteers. Topological data analysis [TDA] examines the structure of data and contributes to the development of medicine, studying properties of a continuous space by the analysis of a discrete sample of it. Using TDA we analyze the topology of Influenzanet data identifying noise and distinguishing higher dimension features. This is done both in terms of the overall structure of a disease as well as its evolution. It provides a way to test agreement at a global scale arising from standard local models. We also compare this qualitative method to other quantitative methods such as Fourier analysis or dynamical time warping [DTW].
The Electromagnetic Counterpart of the Binary Neutron Star Merger LIGO/Virgo GW170817. II. UV, Optical, and Near-infrared Light Curves and Comparison to Kilonova Models

We present UV, optical, and near-infrared (NIR) photometry of the first electromagnetic counterpart to a gravitational wave source from Advanced Laser Interferometer Gravitational-wave Observatory (LIGO)/Virgo, the binary neutron star merger GW170817. Our data set extends from the discovery of the optical counterpart at 0.47–18.5 days post-merger, and includes observations with the Dark Energy Camera (DECam), Gemini-South/FLAMINGOS-2 (GS/F2), and the Hubble Space Telescope (HST). The spectral energy distribution (SED) inferred from this photometry at 0.6 days is well described by a blackbody model with T ≈ 8300 K, a radius of R ≈ 4.5 × 10 14 cm (corresponding to an expansion velocity of v ≈ 0.3 c ), and a bolometric luminosity of L bol ≈ 5 × 10 41 erg s−1. At 1.5 days we find a multi-component SED across the optical and NIR, and subsequently we observe rapid fading in the UV and blue optical bands and significant reddening of the optical/NIR colors. Modeling the entire data set, we find that models with heating from radioactive decay of 56Ni, or those with only a single component of opacity from r-process elements, fail to capture the rapid optical decline and red optical/NIR colors. Instead, models with two components consistent with lanthanide-poor and lanthanide-rich ejecta provide a good fit to the data; the resulting “blue” component has M ej blue ≈ 0.01 M ⊙ and v ej blue ≈ 0.3 c , and the “red” component has M ej red ≈ 0.04 M ⊙ and v ej red ≈ 0.1 c . These ejecta masses are broadly consistent with the estimated r-process production rate required to explain the Milky Way r-process abundances, providing the first evidence that binary neutron star (BNS) mergers can be a dominant site of r-process enrichment.