Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the T‐cell receptor beta chain repertoire in tumor‐infiltrating lymphocytes

Tumor‐infiltrating lymphocytes (TILs) are direct effectors of tumor immunity, and their characterization is important for further development of immunotherapy. Recent advances in high‐throughput sequencing technologies have enabled a comprehensive analysis of T‐cell receptor (TCR) complementarity‐determining region 3 (CDR3) sequences, which may provide information of therapeutic importance. We developed a high‐fidelity target sequencing method with the ability for absolute quantitation, and performed large‐scale sequencing of TCR beta chain (TCRB) CDR3 regions in TILs and peripheral blood lymphocytes (PBLs). The estimated TCRB repertoire sizes of PBLs from four healthy individuals and TILs from four colorectal cancer tissue samples were 608,664–1,003,098 and 90,228–223,757, respectively. The usage of J‐ and V‐regions was similar in PBLs and TILs. Proportions of CDR3 amino acid (aa) sequences occupying more than 0.01% of the total molecular population were 0.33–0.43% in PBLs and 1.3–3.6% in TILs. Additional low coverage sequencing of 15 samples identified five CDR3 aa sequences that were shared by nine patients, one sequence shared by 10 patients, and one sequence shared by 12 patients. The estimated size of the TCRB repertoire in TILs was significantly smaller than that in PBLs. The proportion of abundant species (>0.01%) in TILs was larger than that in PBLs. Shared CDR3 aa sequences represent a response to common antigens, and the identification of such CDR3 sequences may be beneficial in developing clinical biomarkers.
Stroke classification: a personal view.

Because all history is to some extent personal, and because I have been active throughout attempts at classification, I was asked to provide a personal account of stroke subtyping and stroke registries bringing the topic up to date. ### Early Studies Clinicopathological studies during the first half of the 20th century focused on clinical signs in patients who died after stroke. Brain hemorrhages and infarcts were recognized at necropsy, but could they be separated during life? In 1935, Aring and Merritt1 analyzed 245 stroke patients studied clinically and at necropsy at the Boston City Hospital. They reported demographic, epidemiological, historical, and clinical data to determine which features differentiated thrombosis from hemorrhage. Hemorrhages (intracerebral or subarachnoid) were found in 15% of patients and 82% had ischemic infarcts called “thrombotic;” however, only 3% were considered to have cardiogenic embolic brain infarcts. The main features favoring hemorrhage were headache, vomiting, impaired consciousness, progression of the clinical neurological deficit, bloody spinal fluid, and increased spinal fluid pressure.1 This series was biased toward patients with large fatal hemorrhages and infarcts. Later, Dalsgaard-Nielsen2 in Scandinavia compiled a series of 1 000 stroke patients, and clinicians at the Mayo Clinic analyzed series of patients seen during 1945 through 19543 and from 1955 through 1969.4 These studies were based on retrospective chart reviews and all preceded CT. Infarcts were >4-times more common than hemorrhages. Infarcts were classified as embolic only if the patients had rheumatic heart disease or recent myocardial infarction. Rates of brain embolism using these criteria ranged from 3% to 8%. Nonembolic brain infarcts were assumed to be “thrombotic” and related to occlusion of brain supplying large arteries. Carotid and vertebral artery disease in the neck and lacunar infarction were not diagnoses included in any of these early studies. ### The Harvard Stroke Registry5,–,8 In 1971, Howard Bleich, a …
Paired Related Homeobox Protein 1 is a Regulator of Stemness in Adult Neural Stem/Progenitor Cells

Newborn neurons are generated from neural stem cells (NSCs) in two major niches of the adult brain. Maintenance of self-renewal and multipotency of adult NSCs is controlled by multiple transcription factor networks. We show here that paired related homeobox protein Prx1 (MHox1/Prrx1) plays an important role in the maintenance of adult NSCs. Prx1 works with the transcription factor Sox2 as a coactivator, and depletion of Prx1 in cultured adult mouse NSCs reduces their self-renewal. In addition, we find that Prx1 protein is expressed in Sox2+/GFAP+/Nestin+ astrocytes in the germinal regions of the adult mouse forebrain. The continuous expression of Prx1 in proliferating adult mouse hippocampal stem/progenitor cells in vivo leads to the generation of radial/horizontal-shaped astrocyte progenitor- and oligodendrocyte progenitor-like cells with no newborn neurons in the neurogenic niche. These data suggest that Prx1 plays an important role as a key switch for neural cell lineage determination and the maintenance of the self-renewal of adult NSCs at several stages in the adult brain.
Re-forming capitalism

Thirty years after the initiatives of Ronald Reagan and Margaret Thatcher signaled the beginning of a neo-liberal era that would usher in widespread enthusiasm for competitive markets, the world is experiencing a global recession precipitated by financial crises rooted in the excesses of unbridled competition. As a result, the neo liberal era is at an inflection point, if not a close. Many people are reconsidering what markets can deliver and looking again to states for more assertive efforts to regulate and distribute resources. After several decades of irrational exuberance about what markets could accomplish, scholars are looking at capitalism with more sober eyes. In this context, Wolfgang Streeck, the most brilliant analyst of the contemporary German political economy, has produced an indispens able work. It is three books in one a discerning account of recent changes in the German economic model, a wide-ranging critique of institutionalist analysis, and a powerful interpretation of how capital ism works. Written from a profoundly sociological perspective, it offers a corrective to rationalist analyses that will be of interest, not only to scholars of Germany, but to anyone trying to understand institutional change in capitalist economies. Drawing on research carried out under his direction at the Max Planck Institute for the Study of Societies in Cologne, Streeck charts the unraveling over the past twenty years of the "organized capitalism" that once underpinned Modell Deutschland. Five short, sharp chapters trace developments in collective bargaining, intermediary organiza tions, corporate governance, social policy and public finance. In the decade after 1992, net trade union membership in Germany fell from 30 percent of the workforce to about 20 percent. The average tenure of chief executive officers dropped from ten years to eight and a half and, in the largest fifty firms, barely 9 percent of CEOs now have profes sional experience in the public sector, compared with 25 percent in 1990. From an Anglo-American perspective, many aspects of economic relations in Germany still seem relatively "organized". Although only 57 percent of employees were covered by an industry-wide collective agreement in 2006, down from 72 percent in 1995, those figures are still high by international standards, and the wave of hostile takeovers
Cognitive Impairments Induced by Concussive Mild Traumatic Brain Injury in Mouse Are Ameliorated by Treatment with Phenserine via Multiple Non-Cholinergic and Cholinergic Mechanisms

Traumatic brain injury (TBI), often caused by a concussive impact to the head, affects an estimated 1.7 million Americans annually. With no approved drugs, its pharmacological treatment represents a significant and currently unmet medical need. In our prior development of the anti-cholinesterase compound phenserine for the treatment of neurodegenerative disorders, we recognized that it also possesses non-cholinergic actions with clinical potential. Here, we demonstrate neuroprotective actions of phenserine in neuronal cultures challenged with oxidative stress and glutamate excitotoxicity, two insults of relevance to TBI. These actions translated into amelioration of spatial and visual memory impairments in a mouse model of closed head mild TBI (mTBI) two days following cessation of clinically translatable dosing with phenserine (2.5 and 5.0 mg/kg BID x 5 days initiated post mTBI) in the absence of anti-cholinesterase activity. mTBI elevated levels of thiobarbituric acid reactive substances (TBARS), a marker of oxidative stress. Phenserine counteracted this by augmenting homeostatic mechanisms to mitigate oxidative stress, including superoxide dismutase [SOD] 1 and 2, and glutathione peroxidase [GPx], the activity and protein levels of which were measured by specific assays. Microarray analysis of hippocampal gene expression established that large numbers of genes were exclusively regulated by each individual treatment with a substantial number of them co-regulated between groups. Molecular pathways associated with lipid peroxidation were found to be regulated by mTBI, and treatment of mTBI animals with phenserine effectively reversed injury-induced regulations in the ‘Blalock Alzheimer’s Disease Up’ pathway. Together these data suggest that multiple phenserine-associated actions underpin this compound’s ability to ameliorate cognitive deficits caused by mTBI, and support the further evaluation of the compound as a therapeutic for TBI.
A High-Mass Protobinary System in the Hot Core W3(H2O)

We have observed a high-mass protobinary system in the hot core W3(H2O) with the BIMA array. Our continuum maps at wavelengths of 1.4 and 2.8 mm both achieve subarcsecond angular resolutions and show a double-peaked morphology. The angular separation of the two sources is 1. ″19, corresponding to 2.43 × 103 AU at the source distance of 2.04 kpc. The flux densities of the two sources at 1.4 and 2.8 mm have a spectral index of 3, translating to an opacity law of κν ∝ ν. The small spectral indices suggest that grain growth has begun in the hot core. We have also observed five K components of the methyl cyanide (CH3CN) J = 12 → 11 transitions. A radial velocity difference of 2.81 ± 0.10 km s-1 is found toward the two continuum peaks. Interpreting these two sources as binary components in orbit about each other, we find a minimum mass of 22 M☉ for the system. Radiative transfer models are constructed to explain both the continuum and methyl cyanide line observations of each source. Power-law distributions of both density and temperature are derived. Density distributions close to the free-fall value, r-1.5, are found for both components, suggesting continuing accretion. The derived luminosities suggest that the two sources have equivalent zero-age main-sequence (ZAMS) spectral type B0.5-B0. The nebular masses derived from the continuum observations are about 5 M☉ for source A and 4 M☉ for source C. A velocity gradient previously detected may be explained by unresolved binary rotation with a small velocity difference.
Labor Force Composition and Aggregate Fluctuations

This paper studies the role of the labor composition in explaining aggregate fluctuations and accounting for the changes in aggregate volatility. I estimate a constant elasticity of substitution aggregate production function, which allows to distinguish between labour augmenting and total factor productivity shocks. I then break down the aggregate labor contribution to smaller groups and investigate the role of labor composition on aggregate fluctuations. To this end, labour is decomposed by gender, age, education and industry. In all of these dimensions, the labor composition shifted from highly volatile groups to more stable ones over the last 40 years. Through counterfactual simulations I find that these changes account for around 60% of the moderation in aggregate hours and 70% of the moderation in aggregate production. JEL Classification Codes: E23, E25, E32, J21, J23, D33
Structural drivers and social protection: mechanisms of HIV risk and HIV prevention for South African adolescents

Social protection is high on the HIV‐prevention agenda for youth in sub‐Saharan Africa. However, questions remain: How do unconditional cash transfers work? What is the effect of augmenting cash provision with social care? And can “cash plus care” social protection reduce risks for adolescents most vulnerable to infection? This study tackles these questions by first identifying mediated pathways to adolescent HIV risks and then examining potential main and moderating effects of social protection in South Africa.
Some Notes on the Nature of Game Design

The focus of this paper is to have a critical look at the current game design literature through the analytic al lenses of the current state of the art in design research. The aim is not to create yet another prescriptive framework fo r game design but rather an attempt to connect the game de sign studies to general design studies in a stimulating way. We first discuss what has been said about design in general, including industrial and graphic design, engineerin g, architecture, and even software design. We will the n continue discussing game design specifically compar ed to the design in general and point out similarities an d especially differences. This leads us to a somewhat obvious claim that doing game design is an activity similar to any other design field but that the form and the conten t are specific to the game design context. Even though th is claim might sound obvious it has some unexpected consequences: firstly, it grounds game design in the large body o f existing design research and, secondly, it helps in identify ing the crucial activities, forms, contents, and contexts t hat determine the nature of game design. We look at six game design books alongside two distinct but mutually supporting models of design in general . Our focus is in understanding game design as a situated activity and to see how this notion is discussed in the game design literature.
Pulsar PSR B2303+30: a single system of drifting subpulses, moding and nulling

Analyses of multiple pulse sequences of the pulsar PSR B2303+30 reveal two distinct emission modes. One mode (B) follows a steady even-odd pattern and is more intense. The second mode (Q) is characteristically weak, but has intermittent drift bands with a periodicity of approximately 3P 1 /cycle, and nulls much more frequently than the B mode. Both modes occur with roughly equal frequency, and their profiles have a similar single-humped form with a slight asymmetry. Our observations and analyses strongly suggest that the subpulse drift rates in both modes are linked in a series of cycles, which can be modelled as relaxing oscillations in the underlying circulation rate.
A phenomenological study of competing priorities and African American women striving to achieve work-life balance

xiii Chapter 1: The Problem . 1 Background and Statement of the Problem . 1 Significance of the Study . 4 Theoretical Framework . 4 Systems Theory . 5 Contributions of contemporary thought leaders to diversification of systems theory . 6 Life-Story Method . 11 Definition of terms—Life-story method . 11 Research Questions . 12 Summary . 12 Chapter 2: Review of Literature . 13 Cultural Literature: Faith, Values, and Norms . 13 Work: Leadership and Ethics . 17 Charismatic leadership as the genesis . 18 Transformational leadership . 19 Transactional leadership . 22 Servant leadership . 23 Ethics. 24 Family: Motherhood, Feminism, and Womanism . 28 Work-Life Balance. 33 Theoretical Model: Social Identity Theory . 35 Social identity conflicts and categorization strategies . 36 Summary . 38
26] Himanshu A. Sanghavi. a Software Library for Discrete Event Systems and Other Nite State Machine Based Applications. Master's Thesis

22 in the sense that any other converter will further restrict the behavior of the entire system. However, the maximally permissive converter may not have a minimal number of states. Design of such minimal converters is an interesting problem for future research. 21 If the number of states in the converter is p, then the computational complexity of the algorithm is O(m 2 n 2 p 2) since G 6 has O(mnp) states and equally many reachability computations need to be performed. A test converter for the motivating example is shown in Figure 8. The converter adopts 0 1 2 3 4 5 7 6 +d0 +do +d0 +d0 +d1 +d1 +d1 +d1 +d1 +D-A-a0 +d0 +D-A-a1 Figure 8: A test converter the following simple conversion strategy. Initially when one or more data packets with label 0 arrive (event +d0), it removes the label and forwards a single data packet to the receiver (event +D). No action is taken at this point if more copies of the same data packet arrive (due to a sender timeout). When the receiver transmits an acknowledgment (event-A), the converter attaches the label 0 and puts it onto the sender's channel (event-a0). The procedure is repeated when data packets with a diierent label arrive (except for the diierence in the label used). However, if another data packet with the same label arrives (due to a sender timeout or a loss of acknowledgment in the channel), then the same acknowledgment is retransmitted. We have veriied that L(GkC) (where G = P s kP c kQ r) satisses safety, progress, control-lability, and normality, i.e., it is a converter language. Since L(GkC) is obviously nonempty, it follows from Theorem 3 that C is indeed a valid converter. 6 Conclusion In this paper we have studied the problem of designing protocol converters that need to be interposed between a pair of mismatched protocols. Our approach is systematic and is based on the recent theory of supervisory control of discrete event systems. The work presented here provides a new framework for protocol converter designers on one hand, and serves as an application for the supervisory control theorists on the other hand. The basic concepts of controllability, observability, normality, and computation of supremal languages from supervisory control, and safety, and progress from protocol design play important role in the protocol conversion problem. The converter that we derive is maximally permissive 20 …
Bisimulations for Nondeterministic Labeled Markov Processes

We extend the theory of labeled Markov processes with internal nondeterminism, a fundamental concept for the further development of a process theory with abstraction on nondeterministic continuous probabilistic systems. We define nondeterministic labeled Markov processes (NLMP) and provide three definition of bisimulations: a bisimulation following a traditional characterization, a state based bisimulation tailored to our "measurable" non-determinism, and an event based bisimulation. We show the relation between them, including that the largest state bisimulation is also an event bisimulation. We also introduce a variation of the Hennessy-Milner logic that characterizes event bisimulation and that is sound w.r. t. the other bisimulations for arbitrary NLMP. This logic, however, is infinitary as it contains a denumerable $\lor$. We then introduce a finitary sublogic that characterize all bisimulations for image finite NLMP whose underlying measure space is also analytic. Hence, in this setting, all notions of bisimulation we deal with turn out to be equal. Finally, we show that all notions of bisimulations are different in the general case. The counterexamples that separate them turn to be non-probabilistic NLMP.
Solitons and giants in matrix models

We present a method for solving BPS equations obtained in the collective-field approach to matrix models. The method enables us to find BPS solutions and quantum excitations around these solutions in the one-matrix model, and in general for the Calogero model. These semiclassical solutions correspond to giant gravitons described by matrix models obtained in the framework of AdS/CFT correspondence. The two-field model, associated with two types of giant gravitons, is investigated. In this duality-based matrix model we find the finite form of the n-soliton solution. The singular limit of this solution is examined and a realization of open-closed string duality is proposed.
Using Dynamic Geometry Software GeoGebra in Developing Countries: A Case Study of Impressions of Mathematics Teachers in Nepal.

This article describes a professional development initiative for fifteen mathematics teachers in the use of dynamic geometry software GeoGebra. A four-day introductory workshop was given in Nepal to provide an overview of GeoGebra and its possible integration in the teaching/learning of secondary school mathematics there. Teachers’ impressions and beliefs concerning both the training and the software were researched in the context of applicability in Nepalese schools. The potential for using GeoGebra to teach and learn mathematics in Nepal is very large, as evidenced by the participants’ impressions and enthusiasm about, and willingness to use, dynamic geometry software, despite many constraints and difficulties associated with accessing advanced technology.
ASEAN-India Economic, Trade and Integration Relations: Modelling the Challenges and Opportunities

The paper provides a rigorous analysis of ASEAN-India economic, trade and integration relations and presents evidence-based scenarios and policy options for improving these relations in the context of ‘Look East’ policy, ‘economic diplomacy’, globalisation and post-global financial crisis. The proposed options are robust in the sense of statistical efficiency and credible as meeting the Friedman (1953) and Kydland (2006) data-consistency criterion. Several plausible regional and global scenarios to accommodate major opportunities and the challenges for India vis-a-vis the ASEAN will be proposed for evaluation.
Nitric Oxide Synthesis is Modulated by 1,25-Dihydroxyvitamin D3 and Interferon-γ in Human Macrophages after Mycobacterial Infection

Background Little information is available the role of Nitric Oxide (NO) in host defenses during human tuberculosis (TB) infection. We investigated the modulating factor(s) affecting NO synthase (iNOS) induction in human macrophages. Methods Both iNOS mRNA and protein that regulate the growth of mycobacteria were determined using reverase transcriptase-polymerase chain reaction and western blot analysis. The upstream signaling pathways were further investigated using iNOS specific inhibitors. Results Here we show that combined treatment with 1,25-dihydroxyvitamin D3 (1,25-D3) and Interferon (IFN)-γ synergistically enhanced NO synthesis and iNOS expression induced by Mycobacterium tuberculosis (MTB) or by its purified protein derivatives in human monocyte-derived macrophages. Both the nuclear factor-κB and MEK1-ERK1/2 pathways were indispensable in the induction of iNOS expression, as shown in toll like receptor 2 stimulation. Further, the combined treatment with 1,25-D3 and IFN-γ was more potent than either agent alone in the inhibition of intracellular MTB growth. Notably, this enhanced effect was not explained by increased expression of cathelicidin, a known antimycobacterial effector of 1,25-D3. Conclusion These data support a key role of NO in host defenses against TB and identify novel modulating factors for iNOS induction in human macrophages.
Cost Heterogeneity and the Potential Savings from Market-Based Policies

Policy makers and analysts are often faced with situations where it is unclear whether market-based instruments hold real promise of reducing costs, relative to conventional uniform standards. We develop analytic expressions that can be employed with modest amounts of information to estimate the potential cost savings associated with market-based policies, with an application to the environmental policy realm. These simple formulae can identify instruments that merit more detailed investigation. We illustrate the use of these results with an application to nitrogen oxides control by electric utilities in the United States.