Miracle-dz/UniFAR-FTUs huggingface dataset:
The Human CD77− B Cell Population Represents a Heterogeneous Subset of Cells Comprising Centroblasts, Centrocytes, and Plasmablasts, Prompting Phenotypical Revision1

The process of becoming an Ig-producing plasma cell takes the mature B cell through the germinal center, where Ig genes are diversified through somatic hypermutation and class switch recombination. To more clearly define functional characteristics of the germinal center dark zone centroblasts and the light zone centrocytes, we have performed expression analysis of the CD77+ and CD77− populations, because CD77 has been accepted as a discriminator of centroblasts and centrocytes. Our results demonstrated that the CD77+ and the CD77− populations lack functional associated expression programs discriminating the two populations. Both populations are shown to be actively cycling and to share common features associated with cell cycle regulation and DNA maintenance. They are also shown to have an equally active DNA repair program, as well as components involved in somatic hypermutation and class switch recombination. Moreover, the data also demonstrated that the CD77− population comprises cells with an already initiated plasma cell differentiation program. Together this demonstrates that CD77 does not discriminate centroblasts and centrocytes and that the CD77− population represents a heterogeneous subset of cells, comprising centroblasts, centrocytes, and plasmablast.
Synthetic tolerance: three noncoding small RNAs, DsrA, ArcZ and RprA, acting supra-additively against acid stress

Synthetic acid tolerance, especially during active cell growth, is a desirable phenotype for many biotechnological applications. Natively, acid resistance in Escherichia coli is largely a stationary-phase phenotype attributable to mechanisms mostly under the control of the stationary-phase sigma factor RpoS. We show that simultaneous overexpression of noncoding small RNAs (sRNAs), DsrA, RprA and ArcZ, which are translational RpoS activators, increased acid tolerance (based on a low-pH survival assay) supra-additively up to 8500-fold during active cell growth, and provided protection against carboxylic acid and oxidative stress. Overexpression of rpoS without its regulatory 5′-UTR resulted in inferior acid tolerance. The supra-additive effect of overexpressing the three sRNAs results from the impact their expression has on RpoS-protein levels, and the beneficial perturbation of the interconnected RpoS and H-NS networks, thus leading to superior tolerance during active growth. Unlike the overexpression of proteins, overexpression of sRNAs imposes hardly any metabolic burden on cells, and constitutes a more effective strain engineering strategy.
Non-classical Measurement Theory: a Framework for Behavioral Sciences ∗

Instances of non-commutativity are pervasive in human behavior. In this paper, we suggest that psychological properties such as attitudes, values, preferences and beliefs may be suitably described in terms of the mathematical formalism of quantum mechanics. We expose the foundations of nonclassical measurement theory building on a simple notion of orthospace and ortholattice (logic). Two axioms are formulated and the characteristic state-property duality is derived. A last axiom concerned with the impact of measurements on the state takes us with a leap toward the Hilbert space model of Quantum Mechanics. An application to behavioral sciences is proposed. First, we suggest an interpretation of the axioms and basic properties for human behavior. Then we explore an application to decision theory in an example of preference reversal. We conclude by formulating basic ingredients of a theory of actualized preferences based in non-classical measurement theory. JEL: D80, C65, B41
Cardiometabolic Complications after Androgen Deprivation Therapy in a Man with Prostate Cancer: Effects of 3 Years Intermittent Testosterone Supplementation

Androgen deprivation therapy (ADT) for prostate carcinoma (PCa) may cause cardiometabolic complications unless intermittent androgen blockade (IAB) is instituted. An 80-year-old caucasian man was diagnosed intermediate grade (Gleason 4 + 3) PCa and was treated with continuous ADT with triptorelin plus bicalutamide. After 6 months of treatment, he experienced an acute myocardial infarction and 1 month after hospitalization he came to our outpatient clinic for fatigue, weight gain, and hyperglycemia. Due to iatrogenic hypogonadism, we decided to proceed with IAB, but after 3 months ADT withdrawal his serum testosterone (T) was still 0.5 ng/mL. Due to very low concomitant PSA levels (0.1 ng/mL) he was then proposed intermittent T-gel supplementation (Tostrex®) which was initiated according to the following scheme: 6 months on and 3 months off. T-gel dose was titrated tri-weekly in order to achieve T plasma levels below 3.49 ng/mL. After 6 months on, his serum T raised to a mean value of about 2.0 ng/mL without increments in PSA. After overall 12 months on, his serum T peaked to a mean value of 3.0 ng/mL while a delay in PSA rise was seen after 24 months (0.6 ng/mL) but remained stable until the last observation carried forward (LOCF), at 45 months. No clinical and biochemical PCa progression were observed at LOCF. Reversion of iatrogenic metabolic syndrome started after 6 months of T supplementation without using any add-on treatment. This case provides support that once regression of PCa growth is attained, T supplementation may be administered in well differentiated PCa, especially if IAB is not successful in reverting iatrogenic hypogonadism and its associated cardiac and metabolic complications.
The strength of Ramsey Theorem for coloring relatively large sets

We characterize the computational content and the proof-theoretic strength of a Ramsey-type theorem for bi-colorings of so-called {\em exactly large} sets. An {\it exactly large} set is a set $X\subset\Nat$ such that $\card(X)=\min(X)+1$. The theorem we analyze is as follows. For every infinite subset $M$ of $\Nat$, for every coloring $C$ of the exactly large subsets of $M$ in two colors, there exists and infinite subset $L$ of $M$ such that $C$ is constant on all exactly large subsets of $L$. This theorem is essentially due to Pudl\`ak and R\"odl and independently to Farmaki. We prove that --- over Computable Mathematics --- this theorem is equivalent to closure under the $\omega$ Turing jump (i.e., under arithmetical truth). Natural combinatorial theorems at this level of complexity are rare. Our results give a complete characterization of the theorem from the point of view of Computable Mathematics and of the Proof Theory of Arithmetic. This nicely extends the current knowledge about the strength of Ramsey Theorem. We also show that analogous results hold for a related principle based on the Regressive Ramsey Theorem. In addition we give a further characterization in terms of truth predicates over Peano Arithmetic. We conjecture that analogous results hold for larger ordinals.
Interaction of optokinetic and vestibular stimuli in motion perception.

The ssnsation of self-rotation (circularvection) was produced by rotation of a stripe pattern to the left or to the right at constant angular velocity. During circularvection, subjects were randomly accelerated in constant acceleiation steps. Ths major experimental findings are:1. Thresholds for detection of angular acceleration are raised when this acceleration is opposite to the direction of circularvection. Times to detect these accelerations are similarly increased.2. Magnitude estimates of angular velocity show the effect of a visually induced velocity offset which is increased slightly by vestibular responses in the same direction and decreased markedly when the vestibular responses are in the direction opposite to self-rotation.3. Many of the effects of angular acczleration on psrceived velocity are accurately predicted by the adaptation model of the vestibular system. However, an important nonlinear interaction exists whereby Iapidly occurring conflicts between visual and vestibular sensation, esp.
Architecture-Driven Synthesis of Reconfigurable Cells

In this paper, we present a novel method for merging sets of computational patterns into a reconfigurable cell respecting design constraints and optimizing specific design aspects. Each cell can then be used in a run-time reconfigurable processor extension. Our method uses constraint programming to define the pattern merging problem and therefore can easily include design constraints and optimize different design aspects. Experiments carried out on MediaBench test suite indicate 50% average reduction of cell area without increasing critical path.
A novel mutual authentication scheme for USB storage devices

USB (Universal Serial Bus) is one of the most commonly seen interfaces. It stresses the functionality of Plug-and-Play as well as automatic detection and system resource disposition. Therefore, many peripheral applications are derived from this. Within them, storage devices of USB transport interface are most receptive and popular among for users, because of the data transport is increasingly fast and convenient. Unfortunately, the surveillance and management systems targeting to the applications for USB port are not common, and this would result with information flaw in the security. In this paper, we will propose a novel efficient authentication protocol to rectify and enhance the above mentioned problems.
A Model of Psychosocial Hypertension Showing Reversibility and Progression of Cardiovascular Complications

The sequence of pathophysiological changes that can result from the stimulating effects of a sustained disturbance of the social environment was studied in ten colonies of socially deprived mice. Sixteen formerly isolated males were placed with 16 normal females in population cages consisting of seven intercommunicating boxes. Six of these socially disturbed 32-member colonies were terminated after periods of interaction ranging from 2 days to 9 months. The remaining four were terminated a month or more after the males had been returned to individual isolation. Indirect blood pressure measurements, body and heart weights, and sections of hearts and aortas were studied in the males. Following the shorter exposures, blood pressure reverted to normal in a few days. Exposures of 6 months or more were associated with unchanged body weights and sustained increases in heart weight and blood pressure readings. In addition, there was a significant development of aortic arteriosclerosis and myocardial fibrosis. These changes persisted despite prolonged return to isolation.
Upper Bounds on the Rate of LDPC Codes for a Class of Finite-State Markov Channels

In this correspondence, we consider the class of finite-state Markov channels (FSMCs) in which the channel behaves as a binary symmetric channel (BSC) in each state. Upper bounds on the rate of LDPC codes for reliable communication over this class of FSMCs are found. A simple upper bound for all noninverting FSMCs is first derived. Subsequently, tighter bounds are derived for the special case of Gilbert-Elliott (GE) channels. Tighter bounds are also derived over the class of FSMCs considered. The latter bounds hold almost-surely for any sequence of randomly constructed LDPC codes of given degree distributions. Since the bounds are derived for optimal maximum-likelihood decoding, they also hold for belief propagation decoding. Using the derivations of the bounds on the rate, some lower bounds on the density of parity check matrices for given performance over FSMCs are derived
Evaluating strict and conventional left bundle branch block criteria using electrocardiographic simulations.

AIMS Left bundle branch block (LBBB) is a critical predictor of patient benefit from cardiac resynchronization therapy (CRT), but recent studies suggest that one-third of patients diagnosed with LBBB by conventional electrocardiographic (ECG) criteria may have a false-positive diagnosis. In this study, we tested the hypothesis that recently proposed strict LBBB ECG criteria improve specificity in cases of left ventricular hypertrophy (LVH) /dilatation and incomplete LBBB. METHODS AND RESULTS We developed five heart models based on a healthy male with increasing degrees of LV hypertrophy and/or dilation. With each model, we simulated six conduction types: normal conduction, four increments of delayed initiation of LV activation (incomplete LBBB), and complete LBBB. Simulated ECGs were evaluated for the presence of LBBB by conventional (LV conduction delay and QRSd ≥120 ms) and strict ECG criteria (LV conduction delay, QRSd ≥140 ms men or ≥130 ms women, and mid-QRS notching in at least two of the leads I, aVL, V1, V2, V5, and/or V6). Both conventional and strict LBBB criteria had 100% sensitivity. However, conventional criteria falsely diagnosed LBBB in cases with LVH + LV dilated 10 mm, LVH or LV dilated 10 mm combined with LV initiation ≥6 ms after the right ventricle (RV), and with LV dilated 5 mm combined with LV initiation ≥12 ms after RV (48% specificity). Strict LBBB criteria resulted in no false positives (100% specificity). CONCLUSIONS New strict LBBB criteria increase the specificity of complete LBBB diagnosis in the presence of LV hypertrophy/dilatation and incomplete LBBB, which is critical for selecting CRT patients.
The role of acoustic nonlinearity in tissue heating behind a rib cage using a high-intensity focused ultrasound phased array

The goal of this study was to investigate theoretically the effects of nonlinear propagation in a high-intensity focused ultrasound (HIFU) field produced by a therapeutic phased array and the resultant heating of tissue behind a rib cage. Three configurations of focusing were simulated: in water, in water with ribs in the beam path and in water with ribs backed by a layer of soft tissue. The Westervelt equation was used to model the nonlinear HIFU field, and a 1 MHz phased array consisting of 254 circular elements was used as a boundary condition to the model. The temperature rise in tissue was modelled using the bioheat equation, and thermally necrosed volumes were calculated using the thermal dose formulation. The shapes of lesions predicted by the modelling were compared with those previously obtained in in vitro experiments at low-power sonications. Intensity levels at the face of the array elements that corresponded to the formation of high-amplitude shock fronts in the focal region were determined as 10 W cm−2 in the free field in water and 40 W cm−2 in the presence of ribs. It was shown that exposures with shocks provided a substantial increase in tissue heating, and its better spatial localization in the main focal region only. The relative effects of overheating ribs and splitting of the focus due to the periodic structure of the ribs were therefore reduced. These results suggest that utilizing nonlinear propagation and shock formation effects can be beneficial for inducing confined HIFU lesions when irradiating through obstructions such as ribs. Design of compact therapeutic arrays to provide maximum power outputs with lower intensity levels at the elements is necessary to achieve shock wave regimes for clinically relevant sonication depths in tissue.
Comparison of functional MR imaging guidance to electrical cortical mapping for targeting selective motor cortex areas in neuropathic pain: a study based on intraoperative stereotactic navigation.

PURPOSE To assess the concordance between data from functional MR imaging (fMRI) guidance and the intraoperative electrical cortical mapping (iCM) in targeting selective motor cortex areas in refractory neuropathic pain. METHODS Twenty-one patients (11 women and 10 men; mean age, 55.6 years) with refractory central (ischemic, 8 cases) and neuropathic pain (trigeminal neuropathy, 6 cases; syrinx/amputation/plexus trauma, 7 cases) underwent surgery for the implantation of an epidural electrode for chronic motor cortex stimulation (MCS) with general anesthesia and a frameless neuronavigation system used for the image-guided targeting procedure. All patients were studied by preoperative fMRI and epidural iCM with somatosensory evoked potentials and motor cortex stimulodetection. fMRI investigated systematically motor tasks of both hands and that related to the somatic area (foot or tongue) affected by pain. fMRI data were analyzed with the Statistical Parametric Mapping99 software (initial analysis threshold [AT] corresponding to P < .001), registered in the neuronavigation system and correlated intraoperatively with iCM. Matching of fMRI and iCM was specifically examined, focusing the study on hand mapping. RESULTS Concordance between contours of fMRI activation area and iCM in precentral gyrus (mean distance, 3.8 mm) was found in 20/21 patients (95%). Because precision of iCM was suboptimal in 7 patients, concordance for more restrictive values of the AT (P < .0001) was found in only 13 of these 20 patients. Concordance was not found in one patient, as result of image distortion and residual motion artifact. CONCLUSIONS In this study, fMRI guidance provides information that matches those of an independent functional method. These data illustrate the functional accuracy of fMRI guidance for the operative targeting of selective motor cortex areas in neuropathic pain.
Cross-Dressing the Virion: the Transcapsidation of Adeno-Associated Virus Serotypes Functionally Defines Subgroups

ABSTRACT For all adeno-associated virus (AAV) serotypes, 60 monomers of the Vp1, Vp2, and Vp3 structural proteins assemble via an unknown mechanism to form an intact capsid. In an effort to better understand the properties of the capsid monomers and their role in viral entry and infection, we evaluated whether monomers from distinct serotypes can be mixed to form infectious particles with unique phenotypes. This transcapsidation approach consisted of the transfection of pairwise combinations of AAV serotype 1 to 5 helper plasmids to produce mosaic capsid recombinant AAV (rAAV). All ratios (19:1, 3:1, 1:1, 1:3, and 1:19) of these mixtures were able to replicate the green fluorescent protein transgene and to produce capsid proteins. A high-titer rAAV was obtained with mixtures that included either serotype 1, 2, or 3, whereas an rAAV of intermediate titer was obtained from serotype 5 mixtures. Only mixtures containing the AAV4 capsid exhibited reduced packaging capacity. The binding profiles of the mixed-virus preparations to either heparin sulfate (HS) or mucin agarose revealed that only AAV3-AAV5 mixtures at the 3:1 ratio exhibited duality in binding. All other mixtures displayed either an abrupt shift or a gradual alteration in the binding profile to the respective ligand upon increase of a capsid component that conferred either HS or mucin binding. The transduction of cell lines was used to further evaluate the phenotypes of these transcapsidated virions. Three transduction profiles were observed: (i) small to no change regardless of ratio, (ii) a gradual increase in transduction consistent with titration of a second capsid component, or (iii) an abrupt increase in transduction (threshold effect) dependent on the specific ratios used. Interestingly, an unexpected synergistic effect in transduction was observed when AAV1 helper constructs were combined with type 2 or type 3 recipient helpers. Further studies determined that at least two components contributed to this observed synergy: (i) heparin-mediated binding from AAV2 and (ii) an unidentified enhancement activity from AAV1 structural proteins. Using this procedure of mixing different AAV helper plasmids to generate “cross-dressed” AAV virions, we propose an additional means of classifying new AAV serotypes into subgroups based on functional approaches to analyze AAV capsid assembly, receptor-mediated binding, and virus trafficking. Exploitation of this approach in generating custom-designed AAV vectors should be of significant value to the field of gene therapy.
Beamforming for interference mitigation and its implementation on an SDR baseband processor

We present the first implementation of a distributed beam-forming algorithm for interference mitigation on an SDR baseband processor. Co-channel interference (CCI) is becoming a major source of impairments in wireless communications and distributed beamforming is a promising technique to mitigate its negative impact. However, such schemes are challenging to implement in practical scenarios due to their complexity and synchronization requirements. In this paper, we report on implementation of a suboptimal, yet efficient, beamforming scheme for CCI mitigation and present the complexity modeling and algorithm transformations for achieving numerically stability. We also present the fixed-point quantization and the proper mapping on a parallel programmable baseband architecture aimed for software-defined radio (SDR). We optimize this algorithm for a coarse grained reconfigurable array (CGRA) processor and evaluate it in the context of the LTE standard.
Trends in Hospital Admission for Stroke in Calgary

Background: Stroke incidence has fallen since 1950. Recent trends suggest that stroke incidence may be stabilizing or increasing. We investigated time trends in stroke occurrence and in-hospital morbidity and mortality in the Calgary Health Region. Methods: All patients admitted to hospitals in the Calgary Health Region between 1994 and 2002 with a primary discharge diagnosis code (ICD-9 or ICD-10) of stroke were included. In-hospital strokes were also included. Stroke type, date of admission, age, gender, discharge disposition (died, discharged) and in-hospital complications (pneumonia, pulmonary embolism, deep venous thrombosis) were recorded. Poisson and simple linear regression was used to model time trends of occurrence by stroke type and age-group and to extrapolate future time trends. Results: From 1994 to 2002, 11642 stroke events were observed. Of these, 9879 patients (84.8%) were discharged from hospital, 1763 (15.1%) died in hospital, and 591 (5.1%) developed in-hospital complications from pneumonia, pulmonary embolism or deep venous thrombosis. Both in-hospital mortality and complication rates were highest for hemorrhages. Over the period of study, the rate of stroke admission has remained stable. However, total numbers of stroke admission to hospital have faced a significant increase (p=0.012) due to the combination of increases in intracerebral hemorrhage (p=0.021) and ischemic stroke admissions (p=0.011). Sub-arachnoid hemorrhage rates have declined. In-hospital stroke mortality has experienced an overall decline due to a decrease in deaths from ischemic stroke, intracerebral hemorrhage and sub-arachnoid hemorrhage. Conclusion: Although age-adjusted stroke occurrence rates were stable from 1994 to 2002, this is associated with both a sharp increase in the absolute number of stroke admissions and decline in proportional in-hospital mortality. Further research is needed into changes in stroke severity over time to understand the causes of declining in-hospital stroke mortality rates.
Szegő's first limit theorem in terms of a realization of a continuous-time time-varying systems

It is shown that the limit in an abstract version of Szegő’s limit theorem can be expressed in terms of the antistable dynamics of the system. When the system dynamics are regular, it is shown that the limit equals the difference between the antistable Lyapunov exponents of the system and those of its inverse. In the general case, the elements of the dichotomy spectrum give lower and upper bounds.