Miracle-dz/UniFAR-FTUs huggingface dataset:
Transitioning from Agile Development to Enterprise Product Management Agility

By now, your company has made the transition to Scrum. "Sprints", "backlogs", and "retrospectives" are everyday words, but you have discovered the complications that arise within Product Management. Product Owners and Managers who have been scattered across multiple teams are no longer in sync, and at the senior management level, there is not very much visibility into what the Scrum teams are working on unless backlogs are scrutinized. Even then, it is difficult to connect the user stories to management’s high level goals. In addition, cross-product dependencies are not being effectively recognized and managed. The necessity of tracing high level business objectives and portfolio initiatives down to the user story level is essential to any high performing agile development organization. This experience report details how Ultimate Software has successfully transitioned from agile development to an agile enterprise.
Dual Recognition of the Bacterial Chemoreceptor by Chemotaxis-specific Domains of the CheR Methyltransferase*

Adaptation to persisting stimulation is required for highly sensitive detection of temporal changes of stimuli, and often involves covalent modification of receptors. Therefore, it is of vital importance to understand how a receptor and its cognate modifying enzyme(s) modulate each other through specific protein-protein interactions. In the chemotaxis of Escherichia coli, adaptation requires methylation of chemoreceptors (e.g.Tar) catalyzed by the CheR methyltransferase. CheR binds to the C-terminal NWETF sequence of a chemoreceptor that is distinct from the methylation sites. However, little is known about how CheR recognizes its methylation sites or how it is distributed in a cell. In this study, we used comparative genomics to demonstrate that the CheR chemotaxis methyltransferase contains three structurally and functionally distinct modules: (i) the catalytic domain common to a methyltransferase superfamily; (ii) the N-terminal domain; and (iii) the β-subdomain of the catalytic domain, both of which are found exclusively in chemotaxis methyltransferases. The only evolutionary conserved motif specific to CheR is the positively charged face of helix α2 in the N-terminal domain. The disulfide cross-linking analysis suggested that this face interacts with the methylation helix of Tar. We also demonstrated that CheR localizes to receptor clusters at cell poles via interaction of the β-subdomain with the NWETF sequence. Thus, the two chemotaxis-specific modules of CheR interact with distinct regions of the chemoreceptor for targeting to the receptor cluster and for recognition of the substrate sites, respectively.
Local Ablative Therapies in HCC: Percutaneous Ethanol Injection and Radiofrequency Ablation

Hepatocellular carcinoma (HCC) is the most common primary hepatic malignancy. Surgery and transarterial chemoembolization have for many years dominated the local treatment of HCC. The introduction of image-guided percutaneous techniques for local tumor ablation changed the treatment of liver cancer. Percutaneous ethanol injection (PEI) and radiofrequency ablation (RFA) have both successfully been employed in the treatment of HCC. In current guidelines both techniques are recommended as standard therapy in limited liver cancer. From the current literature both techniques have to be considered safe and effective in the treatment of HCC. Several randomized trials showed RFA to be superior to PEI for treating small HCC. Moreover, several studies analyzed survival after PEI or RFA in comparison with surgery, proving interventional therapy to be a serious competitor of resection. With introduction of combined interventional therapies including transarterial chemoembolization, PEI and RFA survival was improved further. In this article, we provide an insight into the technical basics of PEI and RFA and review the clinical results and indications of these interventional techniques in the treatment of HCC.
Nef from primary isolates of human immunodeficiency virus type 1 suppresses surface CD4 expression in human and mouse T cells

The human immunodeficiency virus type 1 (HIV-1) nef gene was originally described as a negative regulator of transcription from the viral long terminal repeat promoter. This observation has been disputed, and the function of Nef remains unclear. In vivo experiments have indicated that an intact nef gene is required for disease progression in macaques infected with simian immunodeficiency virus, suggesting a role for Nef in the pathogenesis of AIDS. We and others have previously shown that expression of Nef in cells bearing surface CD4 results in a sustained decrease in surface CD4 expression. This was demonstrated for Nef from two laboratory strains of HIV-1, Bru and SF2. Because both of these isolates were passaged in vitro prior to molecular cloning and in vitro passage can result in mutations which might alter nef gene function, we have analyzed two primary isolates of Nef for their ability to suppress cell surface CD4 expression. The nef genes of HIV-1 isolates from two patients with fewer than 200 CD4+ T cells per mm3 of blood were introduced into human and mouse T-cell lines by retrovirus-mediated gene transfer. Expression of Nef from both isolates correlated with a decrease in surface expression of both human and mouse CD4. To determine whether the ability to suppress surface CD4 expression is a general function of Nef, we also tested an artificially generated consensus nef gene derived from analysis of 54 patient isolates of HIV-1. Expression of the consensus Nef protein also correlated with decreased cell surface CD4 expression in both mouse and human T-cell lines. These results suggest that the ability to suppress cell surface CD4 expression is an intrinsic feature of HIV-1 Nef.
Outcomes in a nurse-led peripherally inserted central catheter program: a retrospective cohort study.

BACKGROUND Peripherally inserted central catheters (PICCs) provide enormous benefit to patients. However, recent publications have highlighted relatively high PICC-associated complication rates. We report on patient and device outcomes from a nurse-led program. METHODS We performed a retrospective analysis of a prospective cohort of consecutive patients undergoing PICC insertion at The Ottawa Hospital between Jan. 1, 2013 and Dec. 31, 2014. Of the 8314 BioFlo PASV PICCs inserted, we randomly selected a sample of 700 and obtained a complete data set for 656. We measured the cumulative incidence of major complications (catheter-related bloodstream infections and deep vein thrombosis) and use of a thrombolytic to alleviate occlusions. RESULTS The total number of catheter days was 58 486, and the median dwell time 45 days. We observed 4 cases of catheter-related bloodstream infection (0.6% [95% CI 0.17%-1.55%]) (0.07/1000 catheter days). Ten patients (1.5% [95% CI 0.83%-2.78%]) (0.17/1000 catheter days) had catheter-related deep venous thrombosis. At least 1 dose of thrombolytic was required in 75 catheters (11.4% [95% CI 8.61%-13.39]), 31 (7.1%) of the 436 single-lumen catheters and 113 (25.7%) of the 440 lumina of dual-lumen catheters (p < 0.001). INTERPRETATION We attribute our low rates of major complications to a nurse-led expert insertion team, standardized care and maintenance protocols, high insertion volumes, novel catheter material and continuous quality-improvement initiatives that are implemented and evaluated regularly. We conclude that the considerable benefits PICCs provide to patients are attained with a low risk of major complications.
Repetitive transcranial magnetic stimulation improves open field locomotor recovery after low but not high thoracic spinal cord compression‐injury in adult rats

Electromagnetic fields are able to promote axonal regeneration in vitro and in vivo. Repetitive transcranial magnetic stimulation (rTMS) is used routinely in neuropsychiatric conditions and as an atraumatic method to activate descending motor pathways. After spinal cord injury, these pathways are disconnected from the spinal locomotor generator, resulting in most of the functional deficit. We have applied daily 10 Hz rTMS for 8 weeks immediately after an incomplete high (T4–5; n = 5) or low (T10–11; n = 6) thoracic closed spinal cord compression‐injury in adult rats, using 6 high‐ and 6 low‐lesioned non‐stimulated animals as controls. Functional recovery of hindlimbs was assessed using the BBB locomotor rating scale. In the control group, the BBB score was significantly better from the 7th week post‐injury in animals lesioned at T4–5 compared to those lesioned at T10–11. rTMS significantly improved locomotor recovery in T10–11‐injured rats, but not in rats with a high thoracic injury. In rTMS‐treated rats, there was significant positive correlation between final BBB score and grey matter density of serotonergic fibres in the spinal segment just caudal to the lesion. We propose that low thoracic lesions produce a greater functional deficit because they interfere with the locomotor centre and that rTMS is beneficial in such lesions because it activates this central pattern generator, presumably via descending serotonin pathways. The benefits of rTMS shown here suggest strongly that this non‐invasive intervention strategy merits consideration for clinical trials in human paraplegics with low spinal cord lesions. © 2003 Wiley‐Liss, Inc.
Local neighborhood effects on long-term survival of individual trees in a neotropical forest

The survival of approximately 235 000 individual tropical trees and saplings in the 50 ha permanent plot on Barro Colorado Island (BCI), Panama was analyzed over a 13-year interval (1982–1995) as a function of four biotic neighborhood variables: (i) total stem density; (ii) conspecific density; (iii) relative plant size; and (iv) relative species richness. These neighborhood variables were measured in annular rings of width 2.5 m, extending 30 m from a given focal plant, and in one more distant annulus at 47.5–50 m. Because survival was spatially autocorrelated, a Gibbs sampler and a Monte Carlo Markov chain method were used for fitting an autologistic regression model to obtain unbiased estimates of parameter variances for hypothesis testing. After pooling all species at the community level, results showed that all four variables had significant and often strong effects on focal plant survival. Three of the four variables had negative effects on focal plant survival; relative plant size was the only variable with a positive effect (18% increase in the survival odds ratio). The variables with a negative effect on the survival odds ratio, in order of their effect strength in the nearest annulus, were: stem density (a 70% reduction in the survival odds ratio), conspecific density (50% reduction) and species richness (13% reduction). A guild-level analysis revealed considerable heterogeneity among guilds in their responses to these variables. For example, survival of gap species showed a much larger positive response to relative plant size than did survival of shade-tolerant species. Survival of shrub species was positively affected by conspecific density, but canopy tree survival was negatively affected. Conspecific density negatively affected survival of rare species much more strongly than survival of common species. The neighborhood effects of conspecific density disappear within approximately 12–15 m of the focal plant. Although locally strong, the rapid spatial decay of these effects raises unanswered questions about their quantitative contribution to the maintenance of tree diversity on landscape scales in the BCI forest.
A Modified Plane Wave Model for Fast and Accurate Characterization of Layered Media

The accuracy and computational speed of ground penetrating radar (GPR) largely rely on the inverse model implemented. In most cases, both accuracy and processing speed cannot be achieved together because of the inherent limitation of modeling GPR signal in complex media. Full wave models (FWMs) are most promising approaches to characterize multilayered media. However, they are inefficient due to the requirement of significant time for integration over singularity. In this paper, a modified plane wave model (MPWM) is proposed to achieve accuracy and better computational speed. The model is derived based on the analytical solution of an FWM. It is versatile for finding response due to multilayered media. The rigorous analysis has shown the similarity between the proposed model and FWMs with cross-correlation value close to unity across a broad frequency spectrum and large ranges of media parameters. Model inversion is achieved by a novel layer stripping technique followed by a gradient-based method. Testing of layered media in laboratory environment demonstrates that the proposed MPWM has significant advantage over FWMs.
Burst Correction Coding From Low-Density Parity-Check Codes

BURST CORRECTION CODING FROM LOW-DENSITY PARITY-CHECK CODES Wai Han Fong, PhD George Mason University, 2015 Dissertation Director: Dr. Shih-Chun Chang Dissertation Co-Director: Dr. Shu Lin This thesis explores techniques and theoretical bounds on efficiently encodable low-density parity-check (LDPC) codes for correcting single and multiple bursts of erasures and/or errors. The approach is to construct good burst correction codes via superposition techniques from smaller constituent codes, such as product codes and/or use existing codes with newer decodings, such as randomly generated LDPC codes with simple recursive erasure decoding. Another goal is to design codes that perform well in a random error environment as well a bursty environment for some channels that change from one state to the other, i.e. a satellite optical link that suffers from fades due to atmospheric scintillation. Novel decoding approaches are explored, i.e. iterative decoding of constituent codes and/or decoding over the entire code. The motivation for this work is the use of multiple burst correction coding for the following types of applications: 1) optical laser communications where atmospheric turbulence create burst errors; 2) wireless communications where fading is created by multipath, or interference from random impulses and jamming; and 3) packet networks where traffic congestion can create erasure bursts from packet losses. Chapter 1: Introduction This thesis is focused on finding new solutions to the classical problem of burst erasure and burst error control for bursty channels. Bursty channels are the result of correlated errors/erasures patterns. Traditional solutions to the this problem involve implementing Reed-Solomon codes. Specifically, this work is focused on exploiting low-density paritycheck (LDPC) codes to solve this problem. Recently, there have been work in this field, [1–3]. We will explore and extend LDPC codes; and apply these codes to multi-dimensional structures, such as product codes and others, as well as use randomly generated LDPC codes in novel approaches.
Rods and cones in the mouse retina. I. Structural analysis using light and electron microscopy

Rods and cones of the C57BL/6J mouse retina have been examined by light and electron microscopy to distinguish the structural features of the two photoreceptor types. By light microscopy, cone nuclei are conspicuously different from rod nuclei in 1‐2 μm plastic sections. Cone nuclei have an irregularly shaped clump of heterochromatin that appears in single sections to be one to three clumps, whereas rod nuclei are more densely stained and have one large, central clump of heterochromatin. Cone nuclei make up approximately 3%; of the photoreceptor nuclei in both the central and peripheral retina at all ages examined up to 267 days. Cone nuclei are confined to the outer half of the outer nuclear layer, and more than 50%; of the cone nuclei lie adjacent to the outer limiting membrane. By electron microscopy, cones in the mouse retina meet virtually every morphological criterion of mammalian cones. The outer segments are conically shaped. Many, if not all of the outer segment discs are continuous with the outer plasma membrane, whereas almost all of the rod discs are not. Cone outer segments are only about half the length of the rod outer segments, and they are contacted by long, villous pigment epithelial cell processes. The cone inner segment diameter is greater than the outer segment diameter, and the accumulation of mitochondria present at the apical end of the inner segment forms a more conspicuous ellipsoid than in rods. The internal fiber or axon of the cone is larger in diameter than that of the rod, and it terminates in a large synaptic pedicle with multiple ribbon synapses, whereas the rod terminal is a smaller spherule with only a single ribbon synaptic complex.
Improved image de-noising algorithm based on the direction of diffusion

De-noising is a classic problem in image processing, however, keep the image edges and details characteristics and de-noising is a contradiction of the relationship. Based on this defect, in this paper, the curvature and gradient are introduced to improve the operator of direction diffusion, which is able to remove the noise t also makes a good save edge features and details of the role, inhibit noise isolation at the same time. Experimental results show that the image de-noising methods can have good results.
TAR independent activation of the human immunodeficiency virus in phorbol ester stimulated T lymphocytes.

Multiple regulatory elements in the human immunodeficiency virus long terminal repeat (HIV LTR) are required for activation of HIV gene expression. Previous transfection studies of HIV LTR constructs linked to the chloramphenicol acetyltransferase gene indicated that multiple regulatory regions including the enhancer, SP1, TATA and TAR regions were important for HIV gene expression. To characterize these regulatory elements further, mutations in these regions were inserted into both the 5′ and 3′ HIV LTRs and infectious proviral constructs were assembled. These constructs were transfected into either HeLa cells, Jurkat cells or U937 cells in both the presence and absence of phorbol esters which have previously been demonstrated to activate HIV gene expression. Viral gene expression was assayed by the level of p24 gag protein released from cultures transfected with the proviral constructs. Results in all cell lines indicated that mutations of the SP1, TATA and the TAR loop and stem secondary structure resulted in marked decreases in gene expression while mutations of the enhancer motif or TAR primary sequence resulted in only slight decreases. However, viruses containing mutations in either the TAR loop sequences or stem secondary structure which were very defective for gene expression in untreated Jurkat cells, gave nearly wild‐type levels of gene expression in phorbol ester‐treated Jurkat cells but not in phorbol ester‐treated HeLa or U937 cells. High level gene expression of these TAR mutant constructs in phorbol ester‐treated Jurkat cells was eliminated by second site mutations in the enhancer region or by disruption of the tat gene. (ABSTRACT TRUNCATED AT 250 WORDS)
Identification of two cerebral malaria resistance loci using an inbred wild-derived mouse strain

Malaria is a complex infectious disease in which the host/parasite interaction is strongly influenced by host genetic factors. The consequences of plasmodial infections range from asymptomatic to severe complications like the neurological syndrome cerebral malaria induced by Plasmodium falciparum in humans and Plasmodium berghei ANKA in rodents. Mice infected with P. berghei ANKA show marked differences in disease manifestation and either die from experimental cerebral malaria (ECM) or from hemolytic anemia caused by hyperparasitemia (HP). A majority of laboratory mouse strains so far investigated are susceptible to ECM; however, a number of wild-derived inbred strains show resistance. To evaluate the genetic basis of this difference, we crossed a uniquely ECM-resistant, wild-derived inbred strain (WLA) with an ECM susceptible laboratory strain (C57BL/6J). All of the (WLA × C57BL/6J) F1 and 97% of the F2 progeny displayed ECM resistance similar to the WLA strain. To screen for loci contributing to ECM resistance, we analyzed a cohort of mice backcrossed to the C57BL/6J parental strain. A genome wide screening of this cohort provided significant linkage of ECM resistance to marker loci in two genetic regions on chromosome 1 (χ2 = 18.98, P = 1.3 × 10−5) and on chromosome 11 (χ2 = 16.51, P = 4.8 × 10−5), being designated Berr1 and Berr2, respectively. These data provide the first evidence of loci associated with resistance to murine cerebral malaria, which may have important implications for the search for genetic factors controlling cerebral malaria in humans.
Electroretinogram Characteristics and the Spectral Mechanisms of the Median Ocellus and the Lateral Eye in Limulus polyphemus

Electrical responses (ERG) to light flashes of various wavelengths and energies were obtained from the dorsal median ocellus and lateral compound eye of Limulus under dark and chromatic light adaptation. Spectral mechanisms were studied by analyzing (a) response waveforms, e.g. response area, rise, and fall times as functions of amplitude, (b) slopes of amplitude-energy functions, and (c) spectral sensitivity functions obtained by the criterion amplitude method. The data for a single spectral mechanism in the lateral eye are (a) response waveforms independent of wavelength, (b) same slope for response-energy functions at all wavelengths, (c) a spectral sensitivity function with a single maximum near 520 mµ, and (d) spectral sensitivity invariance in chromatic adaptation experiments. The data for two spectral mechanisms in the median ocellus are (a) two waveform characteristics depending on wavelength, (b) slopes of response-energy functions steeper for short than for long wavelengths, (c) two spectral sensitivity peaks (360 and 530–535 mµ) when dark-adapted, and (d) selective depression of either spectral sensitivity peak by appropriate chromatic adaptation. The ocellus is 200–320 times more sensitive to UV than to visible light. Both UV and green spectral sensitivity curves agree with Dartnall's nomogram. The hypothesis is favored that the ocellus contains two visual pigments each in a different type of receptor, rather than (a) various absorption bands of a single visual pigment, (b) single visual pigment and a chromatic mask, or (c) fluorescence. With long duration light stimuli a steady-state level followed the transient peak in the ERG from both types of eyes.
Sleeve monopole antenna with integrated filter for base station applications

The sleeve monopole antenna with an integrated broadband filter is presented for base station applications. The antenna is designed to radiate from 698–960 MHz (low band) and provide band rejection from 1695–2690 MHz (high band). The antenna exhibits return loss better than −15 dB in the low band. The filter exhibits excellent rejection where the worst-case return loss is approximately −0.3 dB in the high band. The filter also reduces peak gain by as much as 50 dBi in the high band.