LLukas22/scidocs huggingface dataset:
Characterization of 1577 primary prostate cancers reveals novel biological and clinicopathologic insights into molecular subtypes.

BACKGROUND
Prostate cancer (PCa) molecular subtypes have been defined by essentially mutually exclusive events, including ETS gene fusions (most commonly involving ERG) and SPINK1 overexpression. Clinical assessment may aid in disease stratification, complementing available prognostic tests.


OBJECTIVE
To determine the analytical validity and clinicopatholgic associations of microarray-based molecular subtyping.


DESIGN, SETTING, AND PARTICIPANTS
We analyzed Affymetrix GeneChip expression profiles for 1577 patients from eight radical prostatectomy cohorts, including 1351 cases assessed using the Decipher prognostic assay (GenomeDx Biosciences, San Diego, CA, USA) performed in a laboratory with Clinical Laboratory Improvements Amendment certification. A microarray-based (m-) random forest ERG classification model was trained and validated. Outlier expression analysis was used to predict other mutually exclusive non-ERG ETS gene rearrangements (ETS(+)) or SPINK1 overexpression (SPINK1(+)).


OUTCOME MEASUREMENTS
Associations with clinical features and outcomes by multivariate logistic regression analysis and receiver operating curves.


RESULTS AND LIMITATIONS
The m-ERG classifier showed 95% accuracy in an independent validation subset (155 samples). Across cohorts, 45% of PCas were classified as m-ERG(+), 9% as m-ETS(+), 8% as m-SPINK1(+), and 38% as triple negative (m-ERG(-)/m-ETS(-)/m-SPINK1(-)). Gene expression profiling supports three underlying molecularly defined groups: m-ERG(+), m-ETS(+), and m-SPINK1(+)/triple negative. On multivariate analysis, m-ERG(+) tumors were associated with lower preoperative serum prostate-specific antigen and Gleason scores, but greater extraprostatic extension (p<0.001). m-ETS(+) tumors were associated with seminal vesicle invasion (p=0.01), while m-SPINK1(+)/triple negative tumors had higher Gleason scores and were more frequent in Black/African American patients (p<0.001). Clinical outcomes were not significantly different among subtypes.


CONCLUSIONS
A clinically available prognostic test (Decipher) can also assess PCa molecular subtypes, obviating the need for additional testing. Clinicopathologic differences were found among subtypes based on global expression patterns.


PATIENT SUMMARY
Molecular subtyping of prostate cancer can be achieved using extra data generated from a clinical-grade, genome-wide expression-profiling prognostic assay (Decipher). Transcriptomic and clinical analysis support three distinct molecular subtypes: (1) m-ERG(+), (2) m-ETS(+), and (3) m-SPINK1(+)/triple negative (m-ERG(-)/m-ETS(-)/m-SPINK1(-)). Incorporation of subtyping into a clinically available assay may facilitate additional applications beyond routine prognosis.
Characterising Lithium-Ion Battery Degradation through the Identification and Tracking of Electrochemical Battery Model Parameters

Lithium-ion (Li-ion) batteries undergo complex electrochemical and mechanical degradation. This complexity is pronounced in applications such as electric vehicles, where highly demanding cycles of operation and varying environmental conditions lead to non-trivial interactions of ageing stress factors. This work presents the framework for an ageing diagnostic tool based on identifying and then tracking the evolution of model parameters of a fundamental electrochemistry-based battery model from non-invasive voltage/current cycling tests. In addition to understanding the underlying mechanisms for degradation, the optimisation algorithm developed in this work allows for rapid parametrisation of the pseudo-two dimensional (P2D), Doyle-Fuller-Newman, battery model. This is achieved through exploiting the embedded symbolic manipulation capabilities and global optimisation methods within MapleSim. Results are presented that highlight the significant reductions in the computational resources required for solving systems of coupled non-linear partial differential equations.
Generation of Plane Spiral OAM Waves Using Traveling-Wave Circular Slot Antenna

Plane spiral orbital angular momentum (OAM) wave is a new form of OAM-carrying electromagnetic wave that propagates along the transverse direction. A traveling-wave circular slot antenna that can generate plane spiral OAM waves is developed and experimentally demonstrated in this letter. The antenna is excited by a 90<inline-formula> <tex-math notation="LaTeX">$^\circ$</tex-math></inline-formula> hybrid coupler. In order to ensure that the OAM waves are propagating along the transverse plane, a ring horn is added outside the antenna. A prototype with OAM states <italic>l = <inline-formula><tex-math notation="LaTeX">$\pm$</tex-math></inline-formula></italic>3 for 10-GHz operation is fabricated and measured. The near-field phase distributions clearly indicate the azimuth phase shifting, and the radiation patterns show the characteristic of transverse propagation, respectively. The proposed antenna provides a novel approach to implement an OAM wireless communication link that has no phase singularity or divergence problem.
Bregman Divergence-Based Regularization for Transfer Subspace Learning

The regularization principals [31] lead approximation schemes to deal with various learning problems, e.g., the regularization of the norm in a reproducing kernel Hilbert space for the ill-posed problem. In this paper, we present a family of subspace learning algorithms based on a new form of regularization, which transfers the knowledge gained in training samples to testing samples. In particular, the new regularization minimizes the Bregman divergence between the distribution of training samples and that of testing samples in the selected subspace, so it boosts the performance when training and testing samples are not independent and identically distributed. To test the effectiveness of the proposed regularization, we introduce it to popular subspace learning algorithms, e.g., principal components analysis (PCA) for cross-domain face modeling; and Fisher's linear discriminant analysis (FLDA), locality preserving projections (LPP), marginal Fisher's analysis (MFA), and discriminative locality alignment (DLA) for cross-domain face recognition and text categorization. Finally, we present experimental evidence on both face image data sets and text data sets, suggesting that the proposed Bregman divergence-based regularization is effective to deal with cross-domain learning problems.
Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms

This paper examine the Euler-Lagrange equations for the solution of the large deformation diffeomorphic metric mapping problem studied in Dupuis et al. (1998) and Trouvé (1995) in which two images I 0, I 1 are given and connected via the diffeomorphic change of coordinates I 0○ϕ−1=I 1 where ϕ=Φ1 is the end point at t= 1 of curve Φ t , t∈[0, 1] satisfying .Φ t =v t (Φ t ), t∈ [0,1] with Φ0=id. The variational problem takes the form $$\mathop {\arg {\text{m}}in}\limits_{\upsilon :\dot \phi _t = \upsilon _t \left( {\dot \phi } \right)} \left( {\int_0^1 {\left\| {\upsilon _t } \right\|} ^2 {\text{d}}t + \left\| {I_0 \circ \phi _1^{ - 1} - I_1 } \right\|_{L^2 }^2 } \right),$$ where ‖v t‖ V is an appropriate Sobolev norm on the velocity field v t(·), and the second term enforces matching of the images with ‖·‖L 2 representing the squared-error norm. In this paper we derive the Euler-Lagrange equations characterizing the minimizing vector fields v t, t∈[0, 1] assuming sufficient smoothness of the norm to guarantee existence of solutions in the space of diffeomorphisms. We describe the implementation of the Euler equations using semi-lagrangian method of computing particle flows and show the solutions for various examples. As well, we compute the metric distance on several anatomical configurations as measured by ∫0 1‖v t‖ V dt on the geodesic shortest paths.
IMCE: Energy-efficient bit-wise in-memory convolution engine for deep neural network

In this paper, we pave a novel way towards the concept of bit-wise In-Memory Convolution Engine (IMCE) that could implement the dominant convolution computation of Deep Convolutional Neural Networks (CNN) within memory. IMCE employs parallel computational memory sub-array as a fundamental unit based on our proposed Spin Orbit Torque Magnetic Random Access Memory (SOT-MRAM) design. Then, we propose an accelerator system architecture based on IMCE to efficiently process low bit-width CNNs. This architecture can be leveraged to greatly reduce energy consumption dealing with convolutional layers and also accelerate CNN inference. The device to architecture co-simulation results show that the proposed system architecture can process low bit-width AlexNet on ImageNet data-set favorably with 785.25μJ/img, which consumes ∼3× less energy than that of recent RRAM based counterpart. Besides, the chip area is ∼4× smaller.
Rate optimization by true motion estimation

In this paper, we propose a rate-optimized motion estimation based on a “true” motion tracker. We observe that piecewise continuous motion field reduces the bit rate for differentially encoded motion vectors. Hence, a neighborhood relaxation method is proposed. In addition, in current MPEG-4 video VM, each video-object-plane (VOP) is individually coded by a block-based approach. The bit rate can be further improved by the removal of redundancy among the block motion vectors within the same VOP. Therefore, we also propose a object-and-block hybrid coding. INTRODUCTION In most video compression algorithms, there is always a tradeoff between picture quality and compression ratio (and computational cost). Generally speaking, the lower the compression ratio, the better the picture quality. Some researchers have attempted to develop new algorithms which can achieve higher picture quality with same amount of bits, or achieve the same picture quality with less bits. It was believed that the less the displaced frame difference (referred to as DFD or mean residue), the less the number of bits for residue, and, then, the less the total bit rate. (The less the distortion as well.) Hence, minimal DFD criterion is widely used. In some coding standards, e.g. H.261, H.263, MPEG-1, MPEG-2, which encode the motion vectors differentially within a slice [4], it is not always true that the less the DFD, the less the bit rate because the total number bits also include the number of bits of coding motion vectors. Those conventional block-matching algorithms (BMAs), which treat the motion estimation problem as an optimization problem on DFD only, could suffer from the high price on the differential coding of motion vectors [2]. Figure 1 shows the bit requirement for different vector difference in H.263 standard. The smaller the difference, the less the bits required. A rate-optimized motion estimation algorithm should take account of the total number of bits: f vig n i argmin f vig fbits DFD v Q bits v bits DFD v Q bits v bits DFDn vn Qn bits vn g (1) where vi is the motion vector of block i, vi vi vi , DFDi vi represents In [4], vi vi prediction of vi. In this paper, we assume prediction of vi vi for simplicity.
dapting the Body Appreciation Scale-2 for Children : A psychometric nalysis of the BAS-2 C mma

Positive body image among adults is related to numerous indicators of well-being. However, no research has explored body appreciation among children. To facilitate our understanding of children’s positive body image, the current study adapts and validates the Body Appreciation Scale-2 (BAS-2; Tylka & WoodBarcalow, 2015a) for use with children. Three hundred and forty-four children (54.4% girls) aged 9–11 completed the adapted Body Appreciation Scale-2 for Children (BAS-2C) alongside measures of body esteem, media influence, body surveillance, mood, and dieting. A sub-sample of 154 participants (62.3% girls) completed the questionnaire 6-weeks later to examine stability (test-retest) reliability. The BAS-2C
European project on osteoarthritis: design of a six-cohort study on the personal and societal burden of osteoarthritis in an older European population

BACKGROUND
Osteoarthritis (OA), the most common form of arthritis, is a major contributor to functional impairment and loss of independence in older persons. The European Project on OSteoArthritis (EPOSA) is a collaborative study involving six European cohort studies on ageing. This project focuses on the personal and societal burden and its determinants of osteoarthritis. This paper describes the design of the project, and presents some descriptive analyses on selected variables across countries.


METHODS/DESIGN
EPOSA is an observational study including pre-harmonized data from European cohort studies (Germany, Italy, the Netherlands, Spain, Sweden and the United Kingdom) on older community-dwelling persons aged 65 to 85 years. In total, 2942 persons were included in the baseline study with a mean age of 74.2 years (SD 5.1), just over half were women (51,9%). The baseline assessment was conducted by a face-to-face interview followed by a clinical examination. Measures included physical, cognitive, psychological and social functioning, lifestyle behaviour, physical environment, wellbeing and care utilisation. The clinical examination included anthropometry, muscle strength, physical performance and OA exam. A follow-up assessment was performed 12-18 months after baseline.


DISCUSSION
The EPOSA study is the first population-based study including a clinical examination of OA, using pre-harmonized data across European countries. The EPOSA study provides a unique opportunity to study the determinants and consequences of OA in general populations of older persons, including both care-seeking and non care-seeking persons.
Desensitization in HLA-incompatible kidney recipients and survival.

BACKGROUND
More than 20,000 candidates for kidney transplantation in the United States are sensitized to HLA and may have a prolonged wait for a transplant, with a reduced transplantation rate and an increased rate of death. One solution is to perform live-donor renal transplantation after the depletion of donor-specific anti-HLA antibodies. Whether such antibody depletion results in a survival benefit as compared with waiting for an HLA-compatible kidney is unknown.


METHODS
We used a protocol that included plasmapheresis and the administration of low-dose intravenous immune globulin to desensitize 211 HLA-sensitized patients who subsequently underwent renal transplantation (treatment group). We compared rates of death between the group undergoing desensitization treatment and two carefully matched control groups of patients on a waiting list for kidney transplantation who continued to undergo dialysis (dialysis-only group) or who underwent either dialysis or HLA-compatible transplantation (dialysis-or-transplantation group).


RESULTS
In the treatment group, Kaplan-Meier estimates of patient survival were 90.6% at 1 year, 85.7% at 3 years, 80.6% at 5 years, and 80.6% at 8 years, as compared with rates of 91.1%, 67.2%, 51.5%, and 30.5%, respectively, for patients in the dialysis-only group and rates of 93.1%, 77.0%, 65.6%, and 49.1%, respectively, for patients in the dialysis-or-transplantation group (P<0.001 for both comparisons).


CONCLUSIONS
Live-donor transplantation after desensitization provided a significant survival benefit for patients with HLA sensitization, as compared with waiting for a compatible organ. By 8 years, this survival advantage more than doubled. These data provide evidence that desensitization protocols may help overcome incompatibility barriers in live-donor renal transplantation. (Funded by the National Institute of Diabetes and Digestive and Kidney Diseases and the Charles T. Bauer Foundation.).
TEACHING AND TRUTH "All You Needed Was Godzilla behind Them" Situating (Racial) Knowledge and Teaching Anna Deavere Smith's Twilight: Los Angeles, 1992

Both the text and the learning environment, connecting community sites, enact the formation of knowledge and interpretation whose insights stem from a juxtaposition of experiences, viewpoints, and histories. Students can thus explore key moments in US racial history and relate them importantly to personal stories, taking them out of the abstract or vague world of the history textbook. This is not to be underestimated: it stems from, and often prompts, continued student curiosity and desire to know and research, to fill gaps in their historical knowledge and in the public memory. Twilight: Los Angeles ’s intense juxtaposition of the personal with the historical fosters and rewards just this kind of curiosity and diligence; it also allows groups of students with different racial and ethnic backgrounds to explore, discuss, interpret, and learn from others’ interpretations of specific historical moments. As one of my students noted in a survey response, ‘I think [ Twilight: Los Angeles ] was a good choice because I didn’t learn about any of this in my earlier education. People need to know about the issues raised in the book because they still matter today.’
Detecting Pneumonia in Chest X-Rays with Supervised Learning

Physicians often use chest X-rays to quickly and cheaply diagnose disease associated with the area. However, it is much more difficult to make clinical diagnoses with chest X-rays than with other imaging modalities such as CT or MRI. With computer-aided diagnosis, physicians can make chest X-ray diagnoses more quickly and accurately. Pneumonia is often diagnosed with chest X-Rays and kills around 50,000 people each year [1]. With computeraided diagnosis of pneumonia specifically, physicians can more accurately and efficiently diagnose the disease. In this project, we hope to train a model using the dataset described below to help physicians in making diagnoses of pneumonia in chest X-Rays. Our problem is thus a binary classification where the inputs are chest X-ray images and the output is one of two classes: pneumonia or non-pneumonia.
Impact of surgeon and volume on extended lymphadenectomy at the time of robot-assisted radical cystectomy: results from the International Robotic Cystectomy Consortium (IRCC).

UNLABELLED
WHAT'S KNOWN ON THE SUBJECT? AND WHAT DOES THE STUDY ADD?: Lymph node dissection and it's extend during robot-assisted radical cystectomy varies based on surgeon related factors. This study reports outcomes of robot-assisted extended lymphadenectomy based on surgeon experience in both academic and private practice settings.


OBJECTIVE
To evaluate the incidence of, and predictors for, extended lymph node dissection (LND) in patients undergoing robot-assisted radical cystectomy (RARC) for bladder cancer, as extended LND is critical for the treatment of bladder cancer but the role of minimally invasive surgery for extended LND has not been well-defined in a multi-institutional setting.


PATIENTS AND METHODS
Used the International Robotic Cystectomy Consortium (IRCC) database. In all, 765 patients who underwent RARC at 17 institutions from 2003 to 2010 were evaluated for receipt of extended LND. Patients were stratified by age, sex, clinical stage, institutional volume, sequential case number, and surgeon volume. Logistic regression analyses were used to correlate variables to the likelihood of undergoing extended LND.


RESULTS
In all, 445 (58%) patients underwent extended LND. Among all patients, a median (range) of 18 (0-74) LNs were examined. High-volume institutions (≥100 cases) had a higher mean LN yield (23 vs 15, P < 0.001). On univariable analysis, surgeon volume, institutional volume, and sequential case number were associated with likelihood of undergoing extended LND. On multivariable analysis, surgeon volume [odds ratio (OR) 3.46, 95% confidence interval (CI) 2.37-5.06, P < 0.001] and institution volume [OR 2.65, 95% CI 1.47-4.78, P = 0.001) were associated with undergoing extended LND.


CONCLUSIONS
Robot-assisted LND can achieve similar LN yields to those of open LND after RC. High-volume surgeons are more likely to perform extended LND, reflecting a correlation between their growing experience and increased comfort with advanced vascular dissection.
Delays and adverse clinical outcomes associated with unrecognized pacing indications.

BACKGROUND
A recent UK audit showed that a significant proportion of patients who received pacemakers had pacing indications previously overlooked, leading to significant delays to pacemaker implantation.


AIM
To investigate the reasons for, and morbidity associated with, overlooked pacing indications.


DESIGN
Prospective observational study in a UK regional pacing centre and its referring district hospitals.


METHODS
Hospital records from referring and implanting centres were reviewed for 95 consecutive patients undergoing first pacemaker implant to determine symptoms, investigations and hospitalisations occurring after documentation of a pacing indication.


RESULTS
Thirty-three of ninety-five patients (35%) had a pacing indication overlooked, which was Class I in 14 patients and Class IIa in 19. Reasons for not making a pacing referral in these patients included: failure to recognize the indication in 14, making adjustments to potentially culprit medication in 15 and requesting additional 'confirmatory' tests in 4. Twenty-six patients (79%) with missed indications experienced adverse events after documentation of an indication, and before receiving a pacemaker: 23 had ongoing symptoms (including one cardiac arrest), three received temporary pacing wires and 18 were hospitalized with symptoms related to cardiac rhythm. Twenty-seven patients (82%) had a total of 38 additional specialist investigations after documentation of a pacing indication.


CONCLUSION
Documentation of an indication for pacing failed to trigger referral for permanent pacing in 35% of patients. This failure led to significant delays, morbidity and use of health service resource, which may have been avoided if timely recognition of the pacing indication had prompted referral. Failure to recognize pacing indications and reassessing symptoms and repeating investigation after changes to medication, often required for the management of associated tachyarrhythmias or other medical conditions, contribute to these delays, perhaps unnecessarily.
Research Guides: Standards, Specifications, Protocols, Methods, and Codes: Organizations

A source for industry standards, standard methods, specifications and codes. Not comprehensive! Commercial and government databases in transportation
FLOW OF TIME IN BST/BCONT MODELS AND RELATED SEMANTICAL OBSERVATIONS

First the Branching Space-time and Branching Continuations models are briefly presented. We compare their properties with the traditional definition of a~Flow of Time from physics and we point out the difficulties this definition in relativistic time. A preliminary solution how to implement the~Flow of Time in the given models is then proposed.