Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence and Risk Factors for Symptomatic Thromboembolic Events after Shoulder Arthroplasty

Deep venous thrombosis and pulmonary embolism after shoulder arthroplasty are not well described. We sought to identify the frequency of deep venous thrombosis and pulmonary embolisms in patients after shoulder arthroplasties to compare these rates with the frequency of deep venous thrombosis and pulmonary embolisms among patients who had total hip and total knee arthroplasties, and to identify associated risk factors. The New York State Department of Health Statewide Planning and Research Cooperative System database was used to identify hospital admissions of patients having shoulder, hip, or knee arthroplasties between 1985 and 2003 with or without an associated diagnostic code for deep venous thrombosis or pulmonary embolism. This resulted in a retrospective cohort of 328,301 procedures. The frequency of deep venous thrombosis was 5.0 per 1000 procedures for shoulder arthroplasties compared with 15.7 for hip arthroplasties and 26.9 for knee arthroplasties. The frequency of pulmonary embolisms was 2.3 for shoulder arthroplasties, 4.2 for hip arthroplasties, and 4.4 for knee arthroplasties. Increasing age, trauma, and cancer were risk factors for thromboembolic events after shoulder arthroplasties. Although the absolute rates of thromboembolic complications were less in patients who had shoulder arthroplasties compared with those of patients who had lower extremity procedures, a larger percentage of these complications were pulmonary embolisms. Perioperative antithrombotic prophylaxis may be beneficial to reduce the frequency of deep venous thrombosis and pulmonary embolisms among patients having shoulder arthroplasties, particularly in higher-risk groups. Level of Evidence: Prognostic study, Level II (retrospective study). See the Guidelines for Authors for a complete description of levels of evidence.
Nonlinear adaptive prediction of nonstationary signals

We describe a computationally efficient scheme for the nonlinear adaptive prediction of nonstationary signals whose generation is governed by a nonlinear dynamical mechanism. The complete predictor consists of two subsections. One performs a nonlinear mapping from the input space to an intermediate space with the aim of linearizing the input signal, and the other performs a linear mapping from the new space to the output space. The nonlinear subsection consists of a pipelined recurrent neural network (PRNN), and the linear section consists of a conventional tapped-delay-line (TDL) filter. The nonlinear adaptive predictor described is of general application. The dynamic behavior of the predictor is demonstrated for the case of a speech signal; for this application, it is shown that the nonlinear adaptive predictor outperforms the traditional linear adaptive scheme in a significant way. >
Analysis of SARS-CoV-2 RNA-Sequences by Interpretable Machine Learning Models

We present an approach to investigate SARS-CoV-2 virus sequences based on alignment-free methods for RNA sequence comparison. In particular, we verify a given clustering result for the GISAID data set, which was obtained analyzing the molecular differences in coronavirus populations by phylogenetic trees. For this purpose, we use alignment-free dissimilarity measures for sequences and combine them with learning vector quantization classifiers for virus type discriminant analysis and classification. Those vector quantizers belong to the class of interpretable machine learning methods, which, on the one hand side provide additional knowledge about the classification decisions like discriminant feature correlations, and on the other hand can be equipped with a reject option. This option gives the model the property of self controlled evidence if applied to new data, i.e. the models refuses to make a classification decision, if the model evidence for the presented data is not given. After training such a classifier for the GISAID data set, we apply the obtained classifier model to another but unlabeled SARS-CoV-2 virus data set. On the one hand side, this allows us to assign new sequences to already known virus types and, on the other hand, the rejected sequences allow speculations about new virus types with respect to nucleotide base mutations in the viral sequences. Author summary The currently emerging global disease COVID-19 caused by novel SARS-CoV-2 viruses requires all scientific effort to investigate the development of the viral epidemy, the properties of the virus and its types. Investigations of the virus sequence are of special interest. Frequently, those are based on mathematical/statistical analysis. However, machine learning methods represent a promising alternative, if one focuses on interpretable models, i.e. those that do not act as black-boxes. Doing so, we apply variants of Learning Vector Quantizers to analyze the SARS-CoV-2 sequences. We encoded the sequences and compared them in their numerical representations to avoid the computationally costly comparison based on sequence alignments. Our resulting model is interpretable, robust, efficient, and has a self-controlling mechanism regarding the applicability to data. This framework was applied to two data sets concerning SARS-CoV-2. We were able to verify previously published virus type findings for one of the data sets by training our model to accurately identify the virus type of sequences. For sequences without virus type information (second data set), our trained model can predict them. Thereby, we observe a new scattered spreading of the sequences in the data space which probably is caused by mutations in the viral sequences.
Learning receptive field properties of complex cells in V1

There are two distinct classes of cells in the primary visual cortex (V1): simple cells and complex cells. One defining feature of complex cells is their spatial phase invariance; they respond strongly to oriented grating stimuli with a preferred orientation but with a wide range of spatial phases. A classical model of complete spatial phase invariance in complex cells is the energy model, in which the responses are the sum of the squared outputs of two linear spatially phase-shifted filters. However, recent experimental studies have shown that complex cells have a diverse range of spatial phase invariance and only a subset can be characterized by the energy model. While several models have been proposed to explain how complex cells could learn to be selective to orientation but invariant to spatial phase, most existing models overlook many biologically important details. We propose a biologically plausible model for complex cells that learns to pool inputs from simple cells based on the presentation of natural scene stimuli. The model is a three-layer network with rate-based neurons that describes the activities of LGN cells (layer 1), V1 simple cells (layer 2), and V1 complex cells (layer 3). The first two layers implement a recently proposed simple cell model that is biologically plausible and accounts for many experimental phenomena. The neural dynamics of the complex cells is modeled as the integration of simple cells inputs along with response normalization. Connections between LGN and simple cells are learned using Hebbian and anti-Hebbian plasticity. Connections between simple and complex cells are learned using a modified version of the Bienenstock, Cooper, and Munro (BCM) rule. Our results demonstrate that the learning rule can describe a diversity of complex cells, similar to those observed experimentally. Author summary Many cortical functions originate from the learning ability of the brain. How the properties of cortical cells are learned is vital for understanding how the brain works. There are many models that explain how V1 simple cells can be learned. However, how V1 complex cells are learned still remains unclear. In this paper, we propose a model of learning in complex cells based on the Bienenstock, Cooper, and Munro (BCM) rule. We demonstrate that properties of receptive fields of complex cells can be learned using this biologically plausible learning rule. Quantitative comparisons between the model and experimental data are performed. Results show that model complex cells can account for the diversity of complex cells found in experimental studies. In summary, this study provides a plausible explanation for how complex cells can be learned using biologically plausible plasticity mechanisms. Our findings help us to better understand biological vision processing and provide us with insights into the general signal processing principles that the visual cortex employs to process visual information.
Linear authentication codes: bounds and constructions

In this paper, we consider a new class of unconditionally secure authentication codes, called linear authentication code (or linear A-code). We show that a linear A-code can be characterised by a family of subspaces of a vector space over a finite field. We then derive an upper bound on the size of source space when other parameters of the systems, that is the size of the key space and the authenticator space, and the deception probability, are fixed. We give constructions that are asymptotically close to the bound and show application of these codes in constructing distributed authentication systems.
Impact of body mass index (BMI) and age on the outcome of the IVF process.

BACKGROUND The goal of this study was to examine the impact of body mass index (BMI) and age on the outcome of the IVF process. MATERIALS AND METHODS This was a retrospective case-control study, of all patients undergoing IVF from 2008-2010 in the Re-Medika IVF Centre. A total of 1238 fresh, non-donor IVF cycles were analyzed, but to minimize the bias, only the first cycle for each patient in that period was analysed (N-920). The patients underwent standard protocols for COH and embryology treatment. In all retrieved oocytes, or in 100% of the cases, the process of fertilization was realized with the method of intracytoplasmic sperm insemination (ICSI). The primary end-point assessed was clinical pregnancy rate. Patients were initially grouped into four BMI categories. The data are presented as frequencies (qualitative data) and as mean±SD (quantitative data). Preliminary comparisons between groups with different BMI were made by the Chi-square and one-way ANOVA test. Because fertility declines with age, there is a Pearson-correlation coefficient to see if BMI depends on age, and the resulting value r=0.15 (p<0.05) showed that BMI is age-dependent, the relationship between them showed multicollinearity. However, the calculated error tolerance of 0.9 indicates stability of the model. Furthermore, to adjust the known fertility decline with age, every response or outcome is analysed by the method of multiple linear (continuous data) or logistic (qualitative data) regression, where the independent variables are taken: BMI, age and BMI interaction×age. RESULTS Increased BMI significantly reduces the chance of clinical pregnancy (normal weight vs. overweight: clinical pregnancy rate: 49.2%, vs. 34.3%). Age, analysed as a single factor, significantly reduces clinical pregnancy rate. Interaction of BMI and age significantly affects clinical pregnancy rate. (BMI vs. BMI×Age vs. Age-p 0,01 vs. 0,001 vs. <0,0001). CONCLUSION Increased body mass of patients entering IVF has a negative impact on the final outcome and certainly reduces the success of the process resulting in reduced clinical pregnancy. Interaction of BMI and age showed a strong significant impact on the outcome of IVF seen through the achievement of clinical pregnancy.
Dispersal and transfer of Staphylococcus aureus in an isolation ward for burned patients

Summary The dispersal of Staphylococcus aureus from burned patients, the relation between nasal carriage by the staff and exposure to airborne Staph. aureus, and the transfer of Staph. aureus-carrying particles within the ward have been studied. The dispersal of Staph. aureus from burned patients was correlated to the size of the burn wound. The median values varied from 21 c.f. u. /m.2/hr. for patients with small burns to 453 c.f. u. /m.2/hr. for extensively burned patients. The size of the dispersed particles appeared to be smaller than that usually found in hospital wards. Carriage of nasal strains by the staff was correlated to the air counts; the number of patient sources did not seem to be of great importance. The transfer of Staph. aureus within the ward was at least 6 to 20 times that which would have been expected if transfer was due to air movement only.
The Proteolytic Fragments of the Alzheimer’s Disease-associated Presenilin-1 Form Heterodimers and Occur as a 100–150-kDa Molecular Mass Complex*

Mutations in the presenilin (PS) genes are linked to early onset familial Alzheimer’s disease (FAD). PS-1 proteins are proteolytically processed by an unknown protease to two stable fragments of ∼30 kDa (N-terminal fragment (NTF)) and ∼20 kDa (C-terminal fragment (CTF)) (Thinakaran, G., Borchelt, D. R., Lee, M. K., Slunt, H. H., Spitzer, L., Kim, G., Ratovitsky, T., Davenport, F., Nordstedt, C., Seeger, M., Hardy, J., Levey, A. I., Gandy, S. E., Jenkins, N. A., Copeland, N. G., Price, D. L., and Sisodia, S. S. (1996) Neuron 17, 181–190). Here we show that the CTF and NTF of PS-1 bind to each other. Fractionating proteins from 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonic acid-extracted membrane preparations by velocity sedimentation reveal a high molecular mass SDS and Triton X-100-sensitive complex of approximately 100–150 kDa. To prove if both proteolytic fragments of PS-1 are bound to the same complex, we performed co-immunoprecipitations using multiple antibodies specific to the CTF and NTF of PS-1. These experiments revealed that both fragments of PS-1 occur as a tightly bound non-covalent complex. Upon overexpression, unclipped wild type PS-1 sediments at a lower molecular weight in glycerol velocity gradients than the endogenous fragments. In contrast, the non-cleavable, FAD-associated PS-1 Δexon 9 sediments at a molecular weight similar to that observed for the endogenous proteolytic fragments. This result may indicate that the Δexon 9 mutation generates a mutant protein that exhibits biophysical properties similar to the naturally occurring PS-1 fragments. This could explain the surprising finding that the Δexon 9 mutation is functionally active, although it cannot be proteolytically processed (Baumeister, R., Leimer, U., Zweckbronner, I., Jakubek, C., Grünberg, J., and Haass, C. (1997) Genes & Function1, 149–159; Levitan, D. , Doyle, T. , Brousseau, D. , Lee, M. , Thinakaran, G. , Slunt, H. , Sisodia, S. , and Greenwald, I. (1996)Proc. Natl. Acad. Sci. U. S. A. 93, 14940–14944). Formation of a high molecular weight complex of PS-1 composed of both endogenous PS-1 fragments may also explain the recent finding that FAD-associated mutations within the N-terminal portion of PS-1 result in the hyperaccumulation not only of the NTF but also of the CTF (Lee, M. K., Borchelt, D. R., Kim, G., Thinakaran, G., Slunt, H. H., Ratovitski, T., Martin, L. J., Kittur, A., Gandy, S., Levey, A. I., Jenkins, N., Copeland, N., Price, D. L., and Sisodia, S. S. (1997) Nat. Med. 3, 756–760). Moreover, these results provide a model to understand the highly regulated expression and processing of PS proteins.
The mechanical characterization of stacked, multilayer graphene cantilevers and plates

The mechanical properties of stacked graphene sheets with varying number of layers are examined. The stacked sheets are assembled by manually combining single layer CVD-grown graphene monolayers, resulting in a turbostratic multilayer graphene with irregular layer spacing greater than crystalline graphite. Due to the presence of multiple layers, the material is analyzed as a plate rather than a membrane. Bending stiffness is determined via the deflection of micron-scale cantilevers, prepared using focused ion beam milling, while in-plane tensile stiffness is characterized through center-loading of edge-supported circular specimens. Computational modeling and established analytical solutions are used to extract material and structural property information, and benchmark measured properties relative to complementary results from indentation tests. Stacked, few-layer CVD-grown graphene retains an in-plane elastic modulus of 350N/m/layer (corresponding to 1.04 TPa for an inter-layer spacing of 0.335nm), suggesting good load-sharing between stacked layers. Width-normalized bending stiffness was unmeasurable for cantilevers of 1 and 3 layers, while cantilevers of 5 and 10 layers had values of 11,100nN·nm and 1.3·106nN·nm respectively.
Clinicians' Experience with and Attitudes toward Discussing Advance Directives with Terminally Ill Patients and Their Families in a Chinese Community.

BACKGROUND Although advance directives (ADs) are already exercised in many Western countries, cultural differences surrounding death and dying may potentially pose challenges to the implementation of ADs in a Chinese community. It is therefore relevant to explore the experience with and attitudes towards ADs of health care professionals, who are trained in Western medicine but working in a Chinese cultural setting. Hong Kong represents a unique setting for this. OBJECTIVE The study objective was to evaluate clinicians' experience with and attitudes towards discussing ADs with terminally ill patients and their families. METHODS In this descriptive pilot study, we conducted a cross-sectional questionnaire survey among doctors working in the largest teaching hospital at the University of Hong Kong. RESULTS Seventy-seven out of 269 doctors working in the surveyed departments completed the questionnaire. The majority of participants (n=72; 94%) indicated willingness to initiate discussions about ADs and 62% (n=48) supported the AD to be recognized as a legally binding document but only 49% (n=38) had past experience of such discussions. CONCLUSIONS Clinicians were generally receptive of the concept of the AD, willing to practice it clinically, and supported its legal recognition. However, AD discussions were an infrequent encounter, hence many clinicians lack experience and are unfamiliar with relevant guidelines. Large-scale studies within the health care professions as well as qualitative studies further exploring potential barriers should follow.
Modulation of an Outer Membrane Protease Contributes to the Virulence Defect of Shigella flexneri Strains Carrying a Mutation in the virK Locus

ABSTRACT The Shigella actin assembly protein IcsA is removed from the bacterial surface by the protease IcsP. We show that decreased intracellular spreading of virK::Tn10 mutants is due in part to significant increases in IcsP and IcsP-mediated cleavage of IcsA and that IcsP expression is a critical determinant of Shigella virulence.
Feast and famine in Antarctica: seasonal physiology in the limpet Nacella concinna

The few studies of Antarctic marine invertebrates that have previously examined seasonal changes in physiology have concentrated on species that cease feeding for extended periods in the austral winter. In contrast, the limpet Nacella concinna (Strebel, 1908) feeds throughout the year. To compare the differing physiological responses demonstrated by a continually feeding species and species that cease feeding during winter we measured seasonal changes in N. concinna faecal egestion, oxygen consumption, O:N ratios, ammonia, urea and primary amine excretion at 4 points in the year. Tissue ash-free dry mass decreased by 47% and faecal egestion 10-fold from summer to winter. Metabolic rates decreased significantly in winter (December, 0.61 +/- 0.04 mumol O-2 h(-1); October, 0.38 +/- 0.04 mumol O-2 h(-1)), but to a much lesser degree than other Antarctic marine invertebrates. Ammonia and urea excretion rates showed significant seasonal variations, while no clear pattern was evident in primary amine excretion. Ammonia excretion decreased during late summer and early winter before increasing in spring (minimum, February, 66.23 +/- 5.72 nmol h(-1); maximum, December, 170.83 +/- 9.50 nmol h(-1)). Urea excretion was low in summer (December, 9.88 +/- 1.60 nmol h(-1)) and maximal (July, 26.70 +/- 4.05 nmol h(-1)) in winter. Urea and primary amine excretion combined accounted for between 10 and 38% of total nitrogen excretion. O:N ratios ranged between 7 and 20 and demonstrated that although protein was the dominant respiratory substrate throughout the year, in late summer and early winter lipids and carbohydrates were also utilised for metabolism. N. concinna has a low degree of metabolic seasonality due to the maintenance of high winter metabolic rates. Although feeding during winter provides some energy, it is insufficient to offset the substantial utilisation of tissue energy stores to balance the metabolic budget.
High-Performance Flexible Hybrid Field-Effect Transistors Based on Cellulose Fiber Paper

In this letter, we report for the first time the use of a sheet of cellulose-fiber-based paper as the dielectric layer used in oxide-based semiconductor thin-film field-effect transistors (FETs). In this new approach, we are using the cellulose-fiber-based paper in an ldquointerstraterdquo structure since the device is built on both sides of the cellulose sheet. Such hybrid FETs present excellent operating characteristics such as high channel saturation mobility,(> 30 cm2 / vs drain-source current on/off modulation ratio of approximately 104, near-zero threshold voltage, enhancement n-type operation, and subthreshold gate voltage swing of 0.8 V/decade. The cellulose-fiber-based paper FETs' characteristics have been measured in air ambient conditions and present good stability, after two months of being processed. The obtained results outpace those of amorphous Si thin-film transistors (TFTs) and rival with the same oxide-based TFTs produced on either glass or crystalline silicon substrates. The compatibility of these devices with large-scale/large-area deposition techniques and low-cost substrates as well as their very low operating bias delineates this as a promising approach to attain high-performance disposable electronics like paper displays, smart labels, smart packaging, RFID, and point-of-care systems for self-analysis in bioapplications, among others.
From bench to clinic

Dr. Ward in his commentary summarized the currently available sperm DNA fragmentation (SDF) tests. He classified the eight SDF assays into four groups based on the different target sites and illustrated the grouping in a diagram to simplify understanding of the readers (1). We would like to supplement, in the following sessions, by (I) further solidifying the current clinical evidence of SDF, and (II) discussing means to move SDF from laboratories to clinics.