Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessing the Difficulty and Time Cost of De-identification in Clinical Narratives

Summary Objective: To characterize the difficulty confronting investigators in removing protected health information (PHI) from cross-discipline, free-text clinical notes, an important challenge to clinical informatics research as recalibrated by the introduction of the US Health Insurance Portability and Accountability Act (HIPAA) and similar regulations. Methods: Randomized selection of clinical narratives from complete admissions written by diverse providers, reviewed using a two-tiered rater system and simple automated regular expression tools. For manual review, two independent reviewers used simple search and replace algorithms and visual scanning to find PHI as defined by HIPAA, followed by an independent second review to detect any missed PHI. Simple automated review was also performed for the “easy” PHI that are number- or date-based. Results: From 262 notes, 2074 PHI, or 7.9 ± 6.1 per note, were found. The average recall (or sensitivity) was 95.9% while precision was 99.6% for single reviewers. Agreement between individual reviewers was strong (ICC = 0.99), although some asymmetry in errors was seen between reviewers (p = 0.001). The automated technique had better recall (98.5%) but worse precision (88.4%) for its subset of identifiers. Manually de-identifying a note took 87.3 ± 61 seconds on average. Conclusions: Manual de-identification of free-text notes is tedious and time-consuming, but even simple PHI is difficult to automatically identify with the exactitude required under HIPAA.
Presence of immunoreactive gonadotropin releasing hormone (GnRH) and its receptor (GnRHR) in rat ovary during pregnancy

The present study aims at quantification of gonadotropin releasing hormone (GnRH) by radioimmunoassay, relative expression of its mRNA by real‐time PCR accompanied by its cellular localization in the rat ovary by immunonohistochemistry (IHC) during different time points of pregnancy. To determine the involvement of endogenous ovarian GnRH in receptor mediated local autocrine/paracrine functions within the ovary, the cell specific localization of the classical receptor for GnRH (GnRHR) in the ovary by IHC and expression pattern of its mRNA were studied during pregnancy. Receptor expression during each time point within the ovary was reconfirmed by Western blot analysis accompanied by densitometric analysis of the signal intensity. Results reveal that the content of ovarian GnRH reaches its maximum on Day 20. The densitometric analysis of GnRHR receptor expression from Western blot study exhibits a decreasing trend by Day 20. Presence of GnRH and GnRHR mRNA in the ovary indicates the local synthesis of both ligand and receptor in the rat ovary. Differential expression of GnRH/GnRHR in the corpus luteum throughout pregnancy strengthens the hypothesis of the involvement of ovarian GnRH in local ovarian functions by receptor‐mediated mechanisms. The expression of GnRH and GnRHR in the atretic antral follicles is indicative of the possible involvement of this decapeptide in processes like follicular atresia. The expression of GnRH/GnRHR in the nonatretic antral follicles and their oocytes requires further in‐depth investigation. Collectively, this study for the first time reveals the presence of endogenous ovarian GnRH/GnRHR supporting their possible involvement in local autocrine/paracrine functions during pregnancy. Mol. Reprod. Dev. 75: 1031–1044, 2007. © 2007 Wiley‐Liss, Inc.
Healing of Achilles Tendon, An Experimental Study: Part 2—Histological, Immunohistological and Ultrasonographic Analysis

In 105 rabbits the course of healing was examined at one, two, four, eight and 12 weeks (21 rabbits per group) after an experimental Achilles tendon rupture. The following treatment modalities were compared: A) primary functional treatment; B) operative functional treatment (resorbable suture); and C) operative functional treatment with fibrin glue. For the functional (after)-treatment a special orthosis was applied. A 7.5 MHz Ultrasound probe was used for ultrasonographic evaluation. The histological specimens were stained in Masson-Goldner and Azan technique. Collagen Type III was depicted immunhistologically. A semiquantitative fibrocyte count was performed. The histological results showed a smooth healing in the primary functional treatment group (A), reaching parallel orientation of collagen fibers at 12 weeks. In the suture group (B), a secondary gapping of the tendon stumps was detectable after one week as in all other groups. In the fibrin group (C), the fibrin was resorbed after four weeks without essential influence to the course of healing. At 12 weeks the histologycal evaluation in all groups showed approximately normal tendon pattern. Immunohistochemically, all groups showed cell-associated positive reactions for type-III collagen after one week with a maximum after two weeks. The semiquantitative fibrocyte count in the primary functional group showed a maximal number after one week. In the fibrin glue and suture groups the maximal number could be found after two weeks. Sonographically an increase in tendon thickness was detectable up to the fourth week in all groups. The secondary gapping of the tendon stumps in the suture group could also be detected sonographically. The echogenicity of the tendon during the course of healing showed increasing homogeneity and parallelism in all groups. At 12 weeks the echogenicity was comparable in all groups. The experiment suggests the equivalence of primary functional treatment to a combination of operative and functional therapy in Achilles tendon rupture.
An improved routing metric based on link states for vehicular ad hoc networks

Greedy forwarding is widely adopted in geographic routing protocols for VANETs since it selects the neighbor that is geographically closer to the destination as the next hop and is considered efficient. Because of the highly dynamic network topology and various impairment of radio signal, the link chosen according to the greedy algorithm regardless of the link state is unstable to a large extent, and frequent retransmissions lead to a waste of the network bandwidth and longer end to end delay. To address the issue, the paper proposed a new routing metric called expected one-transmission advance (EOA) to select the next hop to construct the route. The EOA of a certain node means the expected advance that a packet can make towards the destination through one transmission if choose the node as the next hop. The node with largest EOA is chosen as the intermediate node. The EOA metric balances the efficiency and reliability of the routing. We evaluate the performance of EOA by simulation and the result demonstrates significant reductions of end to end delay and increases of throughput compared to the traditional geographic routing protocol using greedy forwarding.
An overview of radiographic film holders.

OBJECTIVES To provide an overview of radiographic film holders, from their inception in the early 1900s to present day. METHODS A Medline literature search was conducted for dental studies that used keywords that pertain to radiographic film holders. Hand searches of the bibliographies were also conducted. Sixty articles (dating from 1896 to 1998) that describe new or improved film holders are reviewed here. RESULTS From the earliest days of dental radiography, dentists attempted to standardize radiographic images and techniques. The focus of researchers in the 1950s to the 1970s was to develop a film holder that would hold the film and allow easy and predictable alignment of the X-ray tube. As research projects became more dependent on dental radiographic measurements, the focus shifted to producing reproducible radiographic images, from which highly repeatable measurements could be made. CONCLUSION Existing devices have strengths and weaknesses. Readily available devices are adequate for routine clinical use; however, user-friendly and patient-friendly film-holding devices that result in highly reliable and accurate measurements have yet to be introduced.
Human Detection using Projected Edge Feature

— The purpose of this paper is to detect human in images. This paper proposes a method for extracting human body feature descriptors consisting of projected edge component series. The feature descriptor can express appearances and shapes of human with local and global distribution of edges. Our method evaluated with a linear SVM classifier on Daimler-Chrysler pedestrian dataset, and test with various sub-region size. The result shows that the accuracy level of proposed method similar to Histogram of Oriented Gradients(HOG) feature descriptor and feature extraction process is simple and faster than existing methods.
Flow Cytometer Performance Characterization, Standardization and Calibration against CD4 on T Lymphocytes Enables Quantification of Biomarker Expressions for Immunological Applications

There is an urgent need for developing a procedure for biomarker standardization and relative quantificationin clinical laboratories. Measuring the expression levels of cell antigens is critical for the diagnosis of many diseases, e.g. leukemia, lymphoma and immunodeficiency diseases. One of the most significant challenges in flow cytometry is obtaining inter-laboratory and intra-laboratory consistent and reproducible results across multiple cytometer platforms and locations longitudinally over time. To obtain measurement consistency, the target flow cytometer voltages should be optimized to segregate the negative population from the electronic noise, and to keep the brightest positive population within the dynamic range of each detector. Then target values should be determined and transferred to selected cytometers. In this study, we optimized a procedure for instrument standardization across three different flow cytometer platforms from the same vendor and in two different locations. The biomarker quantification was implemented on standardized instruments using CD4 expression on T lymphocytes with a known amount of antibody bound per cell as a quantification standard. Our results on blood cell subset typing and CD19 quantification demonstrated that consistent and reliable results could be accomplished between instruments using the developed procedure. Quantitating the expression levels of certain cell biomarkers relative to a known reference marker before, during, and after therapy would provide important information for monitoring antibody-based therapy and could be potentially used to adjust dosing. Presently, we are implementing this protocol to quantify critical disease biomarkers, and making necessary modifications to the procedure to include instruments from different instrument manufacturers.
Combining Localization with Recognition for Scene Augmentation using a Wearable Camera

Maintaining a time-evolving representation of the 3D environment and pose of a camera provides the geometrical underpinning for several capabilities of value to a wearable vision system. In this paper, established methods for the recognition of feature clusters are used to identify known planar objects, and the instantaneous location of the objects relative to the moving camera is determined from a comparison with a reference view. These locations are incorporated as additional measurements in a process of visual simultaneous localization and mapping, which routinely uses other point features to acquire and maintain a map of the surroundings, irrespective of whether objects are present or not. Continued measurement of these mapped objects improves the accuracy of estimated maps. In the context of wearable (or hand-held) vision, the system's ability to enhance generated maps with known objects enables meaningful automatic annotation of the user's surroundings and increases the utility of the map in augmented reality applications.
Endovascular treatment of ruptured intracranial aneurysms in elderly people.

BACKGROUND AND PURPOSE Endovascular detachable coil is being increasingly used for the treatment of cerebral aneurysms but little information is available about its feasibility and effectiveness in people. We assessed clinical outcomes in elderly patients with ruptured intracranial aneurysms treated with selective embolization. METHODS Between 1996 and 2002, 68 patients aged 65-80 years (mean age, 71 years) were treated by selective embolization with coils. Among them, 34 had a Hunt and Hess (HH) grade of I or II; 15, an HH grade of III; and 19, an HH grade of IV or V. All patients except four were treated within 72 hours after initial bleeding; those four patients had an HH grade of IV or V and were treated at 3-6 weeks after their clinical recovery. Clinical outcomes were assessed by using the Modified Glasgow Outcome Scale. Mean duration of follow-up was 20 months (range, 6-36 months). RESULTS Endovascular treatment resulted in 47 complete occlusions (69%), 15 neck remnants (22%), and six incomplete occlusions (9%). Procedural complications occurred in eight patients (12%). Outcomes were good or excellent in 40 patients (59%), including the four treated 3-6 weeks after initial bleeding. A fair or poor outcome was observed in 14 patients (20.5%), including two with an HH grade of I or II. Of 14 patients (20.5%) who died, 13 (93%) had an HH grade of IV or V. No rebleeding occurred during follow-up. CONCLUSION Endosaccular coiling may be proposed in elderly people with ruptured intracranial aneurysms. However, in patients with HH grade IV or V lesions, morbidity and mortality rates remain high, and embolization should be considered only after their clinical recovery.
5 Epigenetics and Targeted Therapy in Acute Leukemia

Chromatin is a highly ordered structure consisting of repeats of nucleosomes connected by linker DNA. It consists of DNA, histone, and nonhistone proteins condensed into nucleoprotein complexes and it functions as the physiological template of all eukaryotic genetic information. Histones are small basic proteins containing a globular domain and a flexible charged NH2 terminus known as the histone tail, which protrudes from the nucleosome. Epigenetic codes are set up by modifications on the DNA (methylation) or on the histones (acetylation, methylation, phosphorylation, ubiquitination, and ADP ribosylation, etc.), by different classes of enzymes in a precise and targeted manner. Posttranslational modification to histones affects chromatin structure and function resulting in altered gene expression and changes in cell behavior. These modifications do not alter the primary sequence of DNA but have an impact on gene expression regulation, most frequently gene suppression. They lead to pathological states in hematopoietic system resulting in acute leukemia. DNA methylation is catalyzed by DNA methyltransferases (DNMTs), of which three active enzymes have been identified in mammals, namely DNMT1, DNMT3A and DNMT3B. DNMT1 is responsible for maintaining pre-existing methylation patterns during DNA replication, while DNMT3A and DNMT3B are required for initiation of de novo methylation. Acetylation is a reversible process. The balance between acetylation (transcriptional activation) and deacetylation (transcriptional repression) is regulated by histone acetyltransferase (HATs) and histone deacetylases (HDACs) in specific lysine residues in the N-termini of histone tails and/or in transcription factors (eg, p53, E2F1, GATA1, RelA, YY1, and Mad/Max) without directly binding to the DNA (Minucci et al., 2006, Gallinare et al., 2007), and is critical in regulating gene expression. Mammalian HDACs are classified into three classes based on their homology to yeast HDACs. Class I HDACs (HDAC1, 2, 3, 8, and 11) are homologues of Sacharomyces cerevisiae histone deacetylase Rpd 3 (reduced potassium dependency 3) and those with greater similarity to yeast Hda1, are class II HDACs (Gray & Ekstrom, 2001; Gao et al., 2002; Kao et al., 2002). Class III HDACs are called Sirtuins, which are homologoues of yeast sir2 (silence information regulator). Histones can be mono-, di-, or tri-methylated at lysine and arginine residues by HMTs, and the recent identification of histone lysine demethylases such as KDM1/LSD1 and the Jumonji-domain (JMJD)-containing protein family shows that histone
The Direct and Indirect Effects of Paliperidone Extended-release on Depressive Symptoms in Schizoaffective Disorder: A Path Analysis.

BACKGROUND This analysis evaluates improvement in symptoms of depression in patients with schizoaffective disorder administered oral paliperidone extended-release by accounting for the magnitude of direct and indirect (changes in negative and positive symptoms and worsening of extrapyramidal symptoms) treatment effects on depressive symptoms. METHODS Data for this post hoc analysis were drawn from two six-week, randomized, placebo-controlled studies of paliperidone extended-release versus placebo in adult subjects with schizoaffective disorder (N=614; NCT00412373, NCT00397033). Subjects with baseline 17-item Hamilton Rating Scale for Depression scores of 16 or greater were included. Structural equation models (path analyses) were used to separate total effects into direct and indirect effects on depressive symptoms. Change from baseline in 17-item Hamilton Rating Scale for Depression score at the Week 6 end point was the dependent variable; changes in Positive and Negative Syndrome Scale positive and negative factors and Simpson-Angus Scale (to evaluate extrapyramidal symptoms) scores were independent variables. RESULTS At baseline, 332 of 614 (54.1%) subjects had a 17-item Hamilton Rating Scale for Depression score of 16 or greater. Path analysis determined that up to 26.4 percent of the paliperidone extended-release versus placebo effect on depressive symptoms may be attributed to a direct treatment effect, and 45.8 percent and 28.4 percent were mediated indirectly through improvements on positive and negative symptoms, respectively. No effects were identified as mediated through extrapyramidal symptoms changes (-0.7%). CONCLUSION RESULTS of this analysis suggest that paliperidone's effect on depressive symptoms in subjects with schizoaffective disorder participating in two six-week, randomized, placebo-controlled studies is mediated through indirect effects (e.g., positive and negative symptom changes) and a direct treatment effect.
Human resources management and its impact on innovation performance in companies

This study is based on the recent literature concerning the management of Human Resources (HR) and, more specifically, how this may influence innovation in a company. We start with the hypothesis that certain management practices in this area (goal recognition and reward for achievement, team work organisation, the creation of a common language and the sharing of experiences amongst R&D workers, inter alia) will have a positive effect on innovation performance in the firm. The influence of industrial sector to which a firm belongs and the combined application of these politics are also considered. These hypotheses are tested with a survey of 670 innovations developed by the Spanish firms.
Dynamic Server Cluster Load Balancing in Virtualization Environment with OpenFlow

The load balancing technology is widely used in current enterprise network to provide high quality and reliable service. Conventional load balancing technology is often achieved by specific hardware that is usually very expensive and lacks sufficient flexibility. Meanwhile, it is easy to become a single point of failure and would be restricted in virtualization environments. Thus, we propose a load balancing algorithm based on server running state, which can calculate comprehensive loading according to the CPU utilization, memory utilization, and network traffic of the servers. Furthermore, a load balancing solution based on software defined networks (SDN) technology is applied in this paper, and it is designed and implemented in OpenFlow network. We combine network management and server state monitor in this scheme, in which the OpenFlow switches forward the request to the least comprehensive loading server by modifying the packet.
Zero‐recombinant haplotyping: Applications to fine mapping using SNPs

As the number of single nucleotide polymorphisms (SNPs) available for genetic analysis increases, researchers will be saturating smaller and smaller regions of the genome with these biallelic markers in an effort to fine map complex diseases. An important tool in this fine‐mapping effort is haplotyping. Algorithms are presented that find all possible haplotype configurations of the pedigree data under the assumption that there are no recombinants between the markers. These configurations can be used to estimate the haplotype frequencies, and identify the most common haplotypes in the data. These algorithms have been implemented into a software program (ZAPLO), and were tested on a published data set. Genet. Epidemiol. 19(Suppl 1):S64–S70, 2000. © 2000 Wiley‐Liss, Inc.
An Improved EM-Based Design Procedure for Single-Layer Substrate Integrated Waveguide Interconnects with Microstrip Transitions

A practical, computationally efficient technique to EM-based design of single-layer SIW interconnects with microstrip transitions is presented in this work. The design technique efficiently exploits a simplified EM model of the SIW interconnect (surrogate model). The initial design of the SIW structure is obtained by using available empirical equations. A low-resolution EM model with solid walls (grooves) is proposed as an efficient SIW surrogate model for direct EM optimization using a few frequency points. The complete EM optimization of the surrogate model consumes much less time (≪ 20%) than just one simulation of the original EM model (with vias) using a high-resolution grid. The proposed practical technique is illustrated by designing a 10-50 GHz SIW interconnect with microstrip transitions on a standard FR4-based substrate.
Anthropometry and secular changes in stature of urban Colombian women of differing socioeconomic status

Anthropometric dimensions were taken on 1,572 women, 18–44 years of age, from Cali, Colombia, from three different socioeconomic (SEC) groups: low (LEC), mid‐low (MLEC), and upper (UEC). LEC and MLEC women were significantly shorter and had higher body mass indices (BMIs) than UEC women, and a significantly larger number had BMIs over 27.3 kg/m2. There were no significant differences between SEC groups for skinfolds on the arm, but skinfolds on the trunk, the subscapular–triceps ratio, and the waist–hip ratio followed an inverse SEC gradient, indicating a greater tendency for upper body fat distribution in the lower SEC groups. SEC differences in body fatness and fat distribution diminished with age, suggesting that health risks associated with obesity and an upper body fat distribution may be similar in all three groups by ages 40–44 years. Secular changes in stature were similar, 0.12 cm/year for LEC/MLEC women and 0.15 cm/year for UEC women, and there was no indication that the statural differences between the groups is diminishing. The results indicate that women from Cali exhibit anthropometric characteristics seen in both developing countries (stature positively associated with SEC) and developed countries (fatness and centralized fat distribution inversely related to SEC). These findings may reflect the relative economic prosperity of Colombia as a “developing country”. © 1994 Wiley‐Liss, Inc.
Sensitivity of Weights in Combining Forecasts

In the combination of forecasts, weighted averages that attempt to take into account the accuracy of the forecasts and any dependence among forecasts tend to perform poorly in practice. An important factor influencing this performance is the sensitivity, or instability, of the estimated weights used to generate the combined forecast. The intent of this paper is to look at this instability via graphs and the sampling distribution of the weights. Results are developed for the combination of two forecasts and extended to the m -forecast case by viewing the m -forecast case as a sequence of two-forecast combinations.