Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of hematocrit, shear rate, and turbulence on ultrasonic Doppler spectrum from blood

Previous studies of ultrasonic scattering properties of blood using a pulse-echo experimental arrangement show that ultrasonic backscatter from blood is influenced by a number of factors, including hematocrit, shear rate, and the nature of flow. Since the Doppler frequency spectrum from a Doppler flowmeter is derived from echoes backscattered by red blood cells in the flowing blood, it is also undoubtedly a function of these parameters. The effects of these parameters on Doppler spectrum from blood have been investigated using a pulsed Doppler flowmeter. The results agree well with those obtained in previous studies. One important conclusion of this study is that the assumption that the Doppler spectral power density at a frequency in the Doppler spectrum is linearly proportional to the number of red cells flowing at that velocity used in many theoretical models developed to explain the Doppler phenomenon may be erroneous. An alternative is proposed. It is shown that conclusions derived from these theoretical models would remain valid by making this assumption. <<ETX>>
Bitmap algorithms for counting active flows on high speed links

This paper presents a family of bitmap algorithms that address the problem of counting the number of distinct header patterns (flows) seen on a high speed link. Such counting can be used to detect DoS attacks and port scans, and to solve measurement problems. Counting is especially hard when processing must be done within a packet arrival time (8 nsec at OC-768 speeds) and, hence, must require only a small number of accesses to limited, fast memory. A naive solution that maintains a hash table requires several Mbytes because the number of flows can be above a million. By contrast, our new probabilistic algorithms take very little memory and are fast. The reduction in memory is particularly important for applications that run multiple concurrent counting instances. For example, we replaced the port scan detection component of the popular intrusion detection system Snort with one of our new algorithms. This reduced memory usage on a ten minute trace from 50 Mbytes to 5.6 Mbytes while maintaining a 99.77% probability of alarming on a scan within 6 seconds of when the large-memory algorithm would. The best known prior algorithm (probabilistic counting) takes 4 times more memory on port scan detection and 8 times more on a measurement application. Fundamentally, this is because our algorithms can be customized to take advantage of special features of applications such as a large number of instances that have very small counts or prior knowledge of the likely range of the count.
Direct DNA Extraction from Mycobacterium tuberculosis Frozen Stocks as a Reculture-Independent Approach to Whole-Genome Sequencing

ABSTRACT Culturing before DNA extraction represents a major time-consuming step in whole-genome sequencing of slow-growing bacteria, such as Mycobacterium tuberculosis. We report a workflow to extract DNA from frozen isolates without reculturing. Prepared libraries and sequence data were comparable with results from recultured aliquots of the same stocks.
Nonopsonic Phagocytosis of Group C Neisseria meningitidis by Human Neutrophils

ABSTRACT Although complement-mediated bactericidal activity in serum has long been known to be very important in host defense againstNeisseria meningitidis, recent studies have shown that opsonic phagocytosis by neutrophils is also important. The purpose of this study was to determine if endemic group C N. meningitidis strains were susceptible to nonopsonic (complement- and antibody-independent) phagocytosis by human neutrophils, which is a well-described phenomenon for Neisseria gonorrhoeae. Gonococci that possess one or more of a group of heat-modifiable outer membrane proteins (called opacity-associated [Opa] proteins) are phagocytosed by neutrophils in the absence of serum. We found that four serogroup C meningococcal strains bearing the lacto-N-neotetraose (LNnT) structure on lipooligosaccharide (LOS) were phagocytosed by neutrophils in the absence of antibody and active complement. Confocal microscopy confirmed that the organisms were internalized by neutrophils. This susceptibility was not restricted to carrier isolates, since two of the strains were cultured from blood or cerebrospinal fluid. All four strains expressed Opa protein and had relatively less endogenous LOS and capsule sialylation compared to six strains that were resistant to this type of phagocytosis. Nonopsonic phagocytosis of two of the four strains was inhibited by exogenous sialylation of LOS LNnT and the binding of monoclonal antibody to LNnT. However, an isogenic mutant that lacked the LNnT structure was fully susceptible to nonopsonic phagocytosis. We conclude that group C meningococci can be phagocytosed by neutrophils in the absence of antibody and active complement possibly by two different mechanisms. Expression of Opa protein and downregulation of endogenous surface sialic acids analogous to what is seen for N. gonorrhoeae might be necessary for N. meningitidis as well.
Turn It Off! The Effects of Exposure to Male–Male Erotic Imagery on Heterosexuals' Attitudes toward Gay Men

Despite the recent proliferation of lesbian, gay, and bisexual (LGB) thematic content in U.S. media, there have been relatively few empirical investigations examining its impact on heterosexuals’ attitudes toward LGB individuals. This study examined the effect of one type of content, male–male homoerotic imagery, on male and female heterosexuals’ attitudes toward, stereotypes about, and affective reactions to gay men. One hundred ninety-eight undergraduate students were assigned to either a male–male or male–female erotica condition, and their corresponding attitudes toward gay men were assessed. Results revealed that the effect of erotic imagery (male–male vs. male–female) on participants’ stereotype and affect scores differed for men and women at varying levels of sexual anxiety. The implications of these findings are discussed in light of the literature on exposure to erotic imagery and attitudes toward gay men. In particular, the study highlights the need for additional research that acknowledges within-gender heterogeneity with respect to antigay attitude valence, extremity, and function.
Disruption of Laminin β2 Chain Production Causes Alterations in Morphology and Function in the CNS

From the elegant studies of Ramon y Cajal (1909) to the current advances in molecular cloning (e.g., Farber and Danciger, 1997), the retina has served as an ideal model for the entire CNS. We have taken advantage of the well described anatomy, physiology, and molecular biology of the retina to begin to examine the role of the laminins, one component of the extracellular matrix, on the processes of neuronal differentiation and synapse formation in the CNS. We have examined the effect of the deletion of one laminin chain, the β2 chain, on retinal development. The gross development of retinas from laminin β2 chain-deficient animals appears normal, and photoreceptors are formed. However, these retinas exhibit several pathologies: laminin β2 chain-deficient mice display abnormal outer segment elongation, abnormal electroretinograms, and abnormal rod photoreceptor synapses. Morphologically, the outer segments are reduced by 50% in length; the outer plexiform layer of mutant animals is disrupted specifically, because only 7% of observed rod invaginating synapses appear normal, whereas the inner plexiform layer is undisturbed; finally, the rate of apoptosis in the mutant photoreceptor layer is twice that of control mice. Physiologically, the electroretinogram is altered; the amplitude of the b-wave and the slope of the b-wave intensity–response function are both decreased, consistent with synaptic disruption in the outer retina. Together, these results emphasize the prominence of the extracellular matrix and, in particular, the laminins in the development and maintenance of synaptic function and morphogenesis in the CNS.
A sub-optimal sampling based method for path planning

In this paper a search algorithm is proposed to find a sub optimal path for a non-holonomic system. For this purpose the algorithm starts sampling the front part of the vehicle and moves towards the destination with a cost function. The bicycle model is used to define the non-holonomic system and a stability analysis with different integration methods is performed on the dynamics of the system. A proper integration method is chosen with a reasonably large step size in order to decrease the computation time. When the tree is close enough to destination the algorithm returns the path and in order to connect the tree to destination point an optimal control problem using single shooting method is defined. To test the algorithm different scenarios are tested and the simulation results show the success of the algorithm.
Out of Place, Out of Mind: Schema-Driven False Memory Effects for Object-Location Bindings

Events consist of diverse elements, each processed in specialized neocortical networks, with temporal lobe memory systems binding these elements to form coherent event memories. We provide a novel theoretical analysis of an unexplored consequence of the independence of memory systems for elements and their bindings, 1 that raises the paradoxical prediction that schema-driven false memories can act solely on the binding of event elements despite the superior retrieval of individual elements. This is because if 2, or more, schema-relevant elements are bound together in unexpected conjunctions, the unexpected conjunction will increase attention during encoding to both the elements and their bindings, but only the bindings will receive competition with evoked schema-expected bindings. We test our model by examining memory for object-location bindings in recognition (Study 1) and recall (Studies 2 and 3) tasks. After studying schema-relevant objects in unexpected locations (e.g., pan on a stool in a kitchen scene), participants who then viewed these objects in expected locations (e.g., pan on stove) at test were more likely to falsely remember this object-location pairing as correct, compared with participants that viewed a different unexpected object-location pairing (e.g., pan on floor). In recall, participants were more likely to correctly remember individual schema-relevant objects originally viewed in unexpected, as opposed to expected locations, but were then more likely to misplace these items in the original room scene to expected places, relative to control schema-irrelevant objects. Our theoretical analysis and novel paradigm provide a tool for investigating memory distortions acting on binding processes.
Inhibition of lysophosphatidate- and thrombin-induced neurite retraction and neuronal cell rounding by ADP ribosylation of the small GTP-binding protein Rho

Addition of the bioactive phospholipid lysophosphatidic acid (LPA) or a thrombin receptor-activating peptide (TRP) to serum-starved N1E-115 or NG108-15 neuronal cells causes rapid growth cone collapse, neurite retraction, and transient rounding of the cell body. These shape changes appear to be driven by receptor-mediated contraction of the cortical actomyosin system independent of classic second messengers. Treatment of the cells with Clostridium botulinum C3 exoenzyme, which ADP-ribosylates and thereby inactivates the Rho small GTP-binding protein, inhibits LPA- and TRP-induced force generation and subsequent shape changes. C3 also inhibits LPA-induced neurite retraction in PC12 cells. Biochemical analysis reveals that the ADP-ribosylated substrate is RhoA. Prolonged C3 treatment of cells maintained in 10% serum induces the phenotype of serum-starved cells, with initial cell flattening being followed by neurite outgrowth; such C3-differentiated cells fail to retract their neurites in response to agonists. We conclude that RhoA is essential for receptor-mediated force generation and ensuing neurite retraction in N1E-115 and PC12 cells, and that inactivation of RhoA by ADP-ribosylation abolishes actomyosin contractility and promotes neurite outgrowth.
Sim2 prevents entry into the myogenic program by repressing MyoD transcription during limb embryonic myogenesis

The basic helix-loop-helix transcription factor MyoD is a central actor that triggers the skeletal myogenic program. Cell-autonomous and non-cell-autonomous regulatory pathways must tightly control MyoD expression to ensure correct initiation of the muscle program at different places in the embryo and at different developmental times. In the present study, we have addressed the involvement of Sim2 (single-minded 2) in limb embryonic myogenesis. Sim2 is a bHLH-PAS transcription factor that inhibits transcription by active repression and displays enhanced expression in ventral limb muscle masses during chick and mouse embryonic myogenesis. We have demonstrated that Sim2 is expressed in muscle progenitors that have not entered the myogenic program, in different experimental conditions. MyoD expression is transiently upregulated in limb muscle masses of Sim2–/– mice. Conversely, Sim2 gain-of-function experiments in chick and Xenopus embryos showed that Sim2 represses MyoD expression. In addition, we show that Sim2 represses the activity of the mouse MyoD promoter in primary myoblasts and is recruited to the MyoD core enhancer in embryonic mouse limbs. Sim2 expression is non-autonomously and negatively regulated by the dorsalising factor Lmx1b. We propose that Sim2 represses MyoD transcription in limb muscle masses, through Sim2 recruitment to the MyoD core enhancer, in order to prevent premature entry into the myogenic program. This MyoD repression is predominant in ventral limb regions and is likely to contribute to the differential increase of the global mass of ventral muscles versus dorsal muscles.
Optimal base positioning for complex mobile manipulation tasks

This paper presents a novel control architecture for kinematic control of the base and the arm of a vehicle-manipulator system during complex mobile manipulation tasks. Particularly, we address kinematic control of robots operating in the presence of constraints such as plane or entry hole constraints imposed on a point on the manipulator arm and an additional focal point constraint imposed on the base. The focal point constraint guarantees that any camera mounted on the base points in the desired direction. We present a formulation that allows us to represent both types of constraints in the same way by introducing a new set of velocity variables. The main advantage of the proposed approach is that we are able to control the end-effector motion in the normal way using conventional operational space control schemes, and by re-writing the Jacobian matrix we also guarantee that the constraints are satisfied. The most challenging problem with this type of constraints is the extremely complex structure that arises when the constraints are mapped from the operational space to joint space. We solve this by first finding a new set of velocity variables for a point on the robot in the vicinity of the obstacle, and on these new variables we impose a structure which guarantees that the robot does not violate the constraints. We then find a mapping denoted the Constrained Jacobian Matrix from the joint variables to these new velocity variables and use this mapping to find a trajectory in joint space for which the constraints are not violated. We present for the first time the Constrained Jacobian Matrix which imposes kinematic constraints on the base and the chain of the vehicle-manipulator system using the same formalism in both cases.
Socio‐demographic and clinical profile of chronic pain with neuropathic characteristics in sub‐Saharan African elderly

Data on characteristics of neuropathic pain (NP) in sub‐Saharan Africa are scarce, especially in the elderly. We conducted this study to appreciate the socio‐demographic and clinical profile of chronic pain (CP) with neuropathic characteristics in sub‐Saharan African elderly with musculoskeletal pain. From January to December 2011, we performed a cross‐sectional study in all Rheumatology outpatients over 60 years at the Center for Gerontology and Geriatrics, Dakar, Senegal. In this study, we included patients who experienced musculoskeletal pain for 3 months or longer (CP) and with a DN4 score ≥ 4 (NP). A complete clinical examination was performed to make the diagnosis of NP ‘definite’ or ‘probable’, and to identify the aetiologies of NP. During the study period, 698 outpatients were examined. There were 394 out of the 549 patients over 60 years who reported CP. Among them, 28 patients (7.1%) scored ≥4 on the DN4 questionnaire. Female patients, low educational attainment, manual professions, non‐workers and diabetes were associated with NP (p < 0.05). The symptoms described by patients with NP, often intricate, were lumboradiculalgia (n = 9), cervico‐brachial neuralgia (n = 3), polyneuropathy (n = 12) and mononeuropathy (n = 6). The presumed aetiologies in patients with NP were: chronic spine diseases (n = 14), painful diabetic peripheral neuropathy (n = 8), Sjögren's syndrome (n = 1), tarsal tunnel syndrome in rheumatoid arthritis (n = 1) and bone metastasis (n = 1). No aetiology was identified among three patients. Chronic spine diseases associated with radiculopathies and diabetic neuropathy are the main causes of NP, well detected by DN4 questionnaire and clinical examination in Senegalese sub‐Saharan African elderly.
MARKET TRANSPARENCY AND MULTI-CHANNEL STRATEGY: MODELING AND EMPIRICAL ANALYSIS OF ONLINE TRAVEL AGENTS

The Internet has transformed the nature of business-to-consumer transaction-making practices in many industries. Sellers now attract customers with innovative Internet-based selling mechanisms that can reveal or conceal market information. We define market transparency as the availability and accessibility of information about products and prices. Firms can influence market transparency either by designing and implementing their own Internet-based selling mechanism
Changing patterns in the clinical characteristics of Korean patients with breast cancer during the last 15 years.

HYPOTHESIS Breast cancer has become the most common cancer in Korean women in recent years, with continuously increased incidence rates attributed to westernized lifestyles. DESIGN Retrospective case series evaluating the changing patterns of clinical characteristics in breast cancer during the last 15 years. SETTING Hospitalized patients with breast cancer in a university medical center. PATIENTS A total of 5001 breast cancer patients who underwent surgery between July 1989 and March 2004 at the Asan Medical Center. MAIN OUTCOME MEASURE Clinicopathologic data were collected using the online Korea Breast Cancer Registration Program, including factors such as age, symptoms, stage, surgery, reconstruction, risk factors, and survival. RESULTS The median age of patients slightly increased from 44 years in 1991 to 46 years in 2003. The most frequent age group was the fifth decade (41.7%) and premenopausal women younger than 50 years (64.9%). The proportion of asymptomatic patients detected by screening mammography increased from 3.8% in 1991 to 21.0% in 2003 (P<.001). The proportion of early breast cancer (stages 0 and I) increased from 34.2% in 1991 to 48.8% in 2003 (P=.013). Breast-conserving surgery has increased continuously from 5.1% in 1991 to 39.1% in 2003 (P<.001). Twelve percent of all patients who underwent mastectomies had immediate reconstruction, and the proportion showed an increasing trend, especially in skin-sparing mastectomy and transverse rectus abdominis myocutaneous flap reconstruction. Five-year observed survival rates were 84.1%. Five-year survival rates according to stages were as follows: (1) 98.5%, stage 0; (2) 95.3%, stage I; (3) 86.0%, stage II; (4) 65.0%, stage III; and (5) 29.3%, stage IV. The number of patients with specific risk factors, such as early menarche and late first delivery, significantly increased. Of 263 high-risk patients examined for the BRCA mutation, mutations were found in 20 patients (7.6%), with 13 cases with BRCA1 and 7 cases with BRCA2. CONCLUSIONS The present study showed a continuous increase in the number of patients with breast cancer; the proportion of young patients, asymptomatic patients, early breast cancer, breast-conserving surgery, and immediate reconstruction after mastectomy; and the number of patients with risk factors. These results suggest that the clinical characteristics of Korean breast cancer patients reflect the patterns of Western countries.
Implementation and user-centric comparison of a novel adaptation logic for DASH with SVC

The MPEG-DASH standard allows the client-centric access to different representations of video content via the HTTP protocol. The client can flexibly switch between different qualities, i.e., different bit rates and thus avoid waiting times during the video playback due to empty playback buffers. However, quality switches and the playback of lower qualities is perceived by the user which may reduce the Quality of Experience (QoE). Therefore, novel algorithms are required which manage the streaming behavior with respect to the user's requirements and which do not waste network resources. As indicated by recent studies, scalable video coding (SVC) may use the current network and content distribution infrastructure in a more efficient way than with single layer codecs. The contribution of this paper is the design and the implementation of a novel DASH/SVC streaming algorithm. By means of measurements in a test-bed, its performance and benefits are evaluated and compared to existing algorithms from an user-centric view point with objective performance metrics. Our findings show that the proposed algorithm outperforms other DASH mechanisms in terms of video quality, low switching frequency and usage of the available resources in a realistic mobile network scenario. This is a first step towards true QoE management of video streaming in the Internet with DASH and SVC.
Pichia pastoris-expressed dengue 3 envelope-based virus-like particles elicit predominantly domain III-focused high titer neutralizing antibodies

Dengue poses a serious public health risk to nearly half the global population. It causes ~400 million infections annually and is considered to be one of the fastest spreading vector-borne diseases. Four distinct serotypes of dengue viruses (DENV-1, -2, -3, and -4) cause dengue disease, which may be either mild or extremely severe. Antibody-dependent enhancement (ADE), by pre-existing cross-reactive antibodies, is considered to be the major mechanism underlying severe disease. This mandates that a preventive vaccine must confer simultaneous and durable immunity to each of the four prevalent DENV serotypes. Recently, we used Pichia pastoris, to express recombinant DENV-2 E ectodomain, and found that it assembled into virus-like particles (VLPs), in the absence of prM, implicated in the elicitation of ADE-mediating antibodies. These VLPs elicited predominantly type-specific neutralizing antibodies that conferred significant protection against lethal DENV-2 challenge, in a mouse model. The current work is an extension of this approach to develop prM-lacking DENV-3 E VLPs. Our data reveal that P. pastoris-produced DENV-3 E VLPs not only preserve the antigenic integrity of the major neutralizing epitopes, but also elicit potent DENV-3 virus-neutralizing antibodies. Further, these neutralizing antibodies appear to be exclusively directed toward domain III of the DENV-3 E VLPs. Significantly, they also lack discernible ADE potential toward heterotypic DENVs. Taken together with the high productivity of the P. pastoris expression system, this approach could potentially pave the way toward developing a DENV E-based, inexpensive, safe, and efficacious tetravalent sub-unit vaccine, for use in resource-poor dengue endemic countries.