Miracle-dz/UniFAR-FTUs huggingface dataset:
Cellular Stoichiometry of the Components of the Chemotaxis Signaling Complex

ABSTRACT The chemotactic sensory system of Escherichia coli comprises membrane-embedded chemoreceptors and six soluble chemotaxis (Che) proteins. These components form signaling complexes that mediate sensory excitation and adaptation. Previous determinations of cellular content of individual components provided differing and apparently conflicting values. We used quantitative immunoblotting to perform comprehensive determinations of cellular amounts of all components in two E. coli strains considered wild type for chemotaxis, grown in rich and minimal media. Cellular amounts varied up to 10-fold, but ratios between proteins varied no more than 30%. Thus, cellular stoichiometries were almost constant as amounts varied substantially. Calculations using those cellular stoichiometries and values for in vivo proportions of core components in complexes yielded an in vivo stoichiometry for core complexes of 3.4 receptor dimers and 1.6 CheW monomers for each CheA dimer and 2.4 CheY, 0.5 CheZ dimers, 0.08 CheB, and 0.05 CheR per complex. The values suggest a core unit of a trimer of chemoreceptor dimers, a dimer (or two monomers) of kinase CheA, and two CheW. These components may interact in extended arrays and, thus, stoichiometries could be nonintegral. In any case, cellular stoichiometries indicate that CheY could be bound to all signaling complexes and this binding would recruit essentially the entire cellular complement of unphosphorylated CheY, and also that phosphatase CheZ, methylesterase CheB, and methyltransferase CheR would be present at 1 per 2, per 14, and per 20 core complexes, respectively. These characteristic ratios will be important in quantitative treatments of chemotaxis, both experimental and theoretical.
IAP Guidelines for the Surgical Management of Acute Pancreatitis

During 2002 the International Association of Pancreatology developed evidenced-based guidelines on the surgical management of acute pancreatitis. There were 11 guidelines, 10 of which were recommendations grade B and one (the second) grade A. (1) Mild acute pancreatitis is not an indication for pancreatic surgery. (2) The use of prophylactic broad-spectrum antibiotics reduces infection rates in computed tomography-proven necrotizing pancreatitis but may not improve survival. (3) Fine-needle aspiration for bacteriology should be performed to differentiate between sterile and infected pancreatic necrosis in patients with sepsis syndrome. (4) Infected pancreatic necrosis in patients with clinical signs and symptoms of sepsis is an indication for intervention including surgery and radiological drainage. (5) Patients with sterile pancreatic necrosis (with negative fine-needle aspiration for bacteriology) should be managed conservatively and only undergo intervention in selected cases. (6) Early surgery within 14 days after onset of the disease is not recommended in patients with necrotizing pancreatitis unless there are specific indications. (7) Surgical and other forms of interventional management should favor an organ-preserving approach, which involves debridement or necrosectomy combined with a postoperative management concept that maximizes postoperative evacuation of retroperitoneal debris and exudate. (8) Cholecystectomy should be performed to avoid recurrence of gallstone-associated acute pancreatitis. (9) In mild gallstone-associated acute pancreatitis, cholecystectomy should be performed as soon as the patient has recovered and ideally during the same hospital admission. (10) In severe gallstone-associated acute pancreatitis, cholecystectomy should be delayed until there is sufficient resolution of the inflammatory response and clinical recovery. (11) Endoscopic sphincterotomy is an alternative to cholecystectomy in those who are not fit to undergo surgery in order to lower the risk of recurrence of gallstone-associated acute pancreatitis. There is however a theoretical risk of introducing infection into sterile pancreatic necrosis. These guidelines should now form the basis for audit studies in order to determine the quality of patient care delivery.
The MSX1 homeobox transcription factor is a downstream target of PHOX2B and activates the Delta-Notch pathway in neuroblastoma

Neuroblastoma is an embryonal tumour of the peripheral sympathetic nervous system (SNS). One of the master regulator genes for peripheral SNS differentiation, the homeobox transcription factor PHOX2B, is mutated in familiar and sporadic neuroblastomas. Here we report that inducible expression of PHOX2B in the neuroblastoma cell line SJNB-8 down-regulates MSX1, a homeobox gene important for embryonic neural crest development. Inducible expression of MSX1 in SJNB-8 caused inhibition of both cell proliferation and colony formation in soft agar. Affymetrix micro-array and Northern blot analysis demonstrated that MSX1 strongly up-regulated the Delta-Notch pathway genes DLK1, NOTCH3, and HEY1. In addition, the proneural gene NEUROD1 was down-regulated. Western blot analysis showed that MSX1 induction caused cleavage of the NOTCH3 protein to its activated form, further confirming activation of the Delta-Notch pathway. These experiments describe for the first time regulation of the Delta-Notch pathway by MSX1, and connect these genes to the PHOX2B oncogene, indicative of a role in neuroblastoma biology. Affymetrix micro-array analysis of a neuroblastic tumour series consisting of neuroblastomas and the more benign ganglioneuromas showed that MSX1, NOTCH3 and HEY1 are more highly expressed in ganglioneuromas. This suggests a block in differentiation of these tumours at distinct developmental stages or lineages
Cartesian genetic programming

Cartesian Genetic Programming is a form of genetic programming. It is increasing in popularity. It was developed by Julian Miller with Peter Thomson in 1997. In its classic form it uses a very simple integer based genetic representation of a program in the form of a directed graph. In a number of studies, it has been shown to be efficient in comparison with other GP techniques. Since then, the classical form of CGP has been enhanced in various ways by including automatically defined functions. Most recently, it has been developed by Julian Miller, Wolfgang Banzhaf and Simon Harding to include self-modification operators. This again has increased its efficiency. The tutorial will cover the basic technique, advanced developments and applications to a variety of problem domains.
Angiotensin II inhibits rat arterial KATP channels by inhibiting steady‐state protein kinase A activity and activating protein kinase Ce

1 We used whole‐cell patch clamp to investigate steady‐state activation of ATP‐sensitive K+ channels (KATP) of rat arterial smooth muscle by protein kinase A (PKA) and the pathway by which angiotensin II (Ang II) inhibits these channels. 2 Rp‐cAMPS, an inhibitor of PKA, did not affect KATP currents activated by pinacidil when the intracellular solution contained 0.1 mM ATP. However, when ATP was increased to 1.0 mM, inhibition of PKA reduced KATP current, while the phosphatase inhibitor calyculin A caused a small increase in current. 3 Ang II (100 nM) inhibited KATP current activated by the K+ channel opener pinacidil. The degree of inhibition was greater with 1.0 mM than with 0.1 mM intracellular ATP. The effect of Ang II was abolished by the AT1 receptor antagonist losartan. 4 The inhibition of KATP currents by Ang II was abolished by a combination of PKA inhibitor peptide 5‐24 (5 μM) and PKC inhibitor peptide 19‐27 (100 μM), while either alone caused only partial block of the effect. 5 In the presence of PKA inhibitor peptide, the inhibitory effect of Ang II was unaffected by the PKC inhibitor Gö 6976, which is selective for Ca2+‐dependent isoforms of PKC, but was abolished by a selective peptide inhibitor of the translocation of the ε isoform of PKC. 6 Our results indicate that KATP channels are activated by steady‐state phosphorylation by PKA at normal intracellular ATP levels, and that Ang II inhibits the channels both through activation of PKCε and inhibition of PKA.
Internal Transcribed Spacer Dimorphism and Diversity in Dientamoeba fragilis

ABSTRACT. The internal transcribed spacer (ITS) region of the ribosomal RNA operon is frequently used for detecting sequence variation among closely related species as it is usually homogeneous within strains but evolves more rapidly than ribosomal RNA coding regions. We have studied this region in both genotypes of the human intestinal parasite Dientamoeba fragilis. In contrast to most organisms, we have identified extensive variation between copies of the sequence within the same strain. The ITS occurs in 2 major forms in each genotype but additional heterogeneity is also present within each form. The significance of this finding is unclear, but the only precedent for such variation is in the Apicomplexa, which have multiple dispersed ribosomal RNA operons in contrast to the tandem arrays found in most other eukaryotes.
Extracting a Climate Signal from 169 Glacier Records

I constructed a temperature history for different parts of the world from 169 glacier length records. Using a first-order theory of glacier dynamics, I related changes in glacier length to changes in temperature. The derived temperature histories are fully independent of proxy and instrumental data used in earlier reconstructions. Moderate global warming started in the middle of the 19th century. The reconstructed warming in the first half of the 20th century is 0.5 kelvin. This warming was notably coherent over the globe. The warming signals from glaciers at low and high elevations appear to be very similar.
Suppression of RNA synthesis by a specific antiviral activity in Sindbis virus-infected Aedes albopictus cells

An antiviral protein is released by mosquito cells persistently infected with Sindbis virus. Differences in both sensitivity to and production of this virus-specific activity were apparent in three independently produced Aedes albopictus cell lines. This activity inhibits total viral RNA synthesis in a time-dependent manner. The antiviral effect is maximally realized when cells are treated with the activity 48 h before infections. These data suggest that the antiviral activity induces an antiviral state in treated cells which prevents the formation or efficient function of viral RNA-synthesizing complexes.
The regulatory T cell effector molecule fibrinogen‐like protein 2 is necessary for the development of rapamycin‐induced tolerance to fully MHC‐mismatched murine cardiac allografts

Therapies that promote tolerance in solid organ transplantation will improve patient outcomes by eliminating the need for long‐term immunosuppression. To investigate mechanisms of rapamycin‐induced tolerance, C3H/HeJ mice were heterotopically transplanted with MHC‐mismatched hearts from BALB/cJ mice and were monitored for rejection after a short course of rapamycin treatment. Mice that had received rapamycin developed tolerance with indefinite graft survival, whereas untreated mice all rejected their grafts within 9 days. In vitro, splenic mononuclear cells from tolerant mice maintained primary CD4+ and CD8+ immune responses to donor antigens consistent with a mechanism that involves active suppression of immune responses. Furthermore, infection with lymphocytic choriomeningitis virus strain WE led to loss of tolerance suggesting that tolerance could be overcome by infection. Rapamycin‐induced, donor‐specific tolerance was associated with an expansion of regulatory T (Treg) cells in both the spleen and allograft and elevated plasma levels of fibrinogen‐like protein 2 (FGL2). Depletion of Treg cells with anti‐CD25 (PC61) and treatment with anti‐FGL2 antibody both prevented tolerance induction. Tolerant allografts were populated with Treg cells that co‐expressed FGL2 and FoxP3, whereas rejecting allografts and syngeneic grafts were nearly devoid of dual‐staining cells. We examined the utility of an immunoregulatory gene panel to discriminate between tolerance and rejection. We observed that Treg‐associated genes (foxp3, lag3, tgf‐β and fgl2) had increased expression and pro‐inflammatory genes (ifn‐γ and gzmb) had decreased expression in tolerant compared with rejecting allografts. Taken together, these data strongly suggest that Treg cells expressing FGL2 mediate rapamycin‐induced tolerance. Furthermore, a gene biomarker panel that includes fgl2 can distinguish between rejecting and tolerant grafts.
Microvariation in Accentual Alignment in Basque Spanish

This paper presents patterns of accentual alignment in two varieties of Spanish spoken in the Basque Country: Lekeitio Spanish (LS), with speakers whose other native language is Lekeitio Basque (LB); and Vitoria Spanish (VS), with monolingual speakers of Spanish from the city of Vitoria. These patterns are compared to those of Madrid Spanish (MS), compare Face (2002). In LS, accents are realized as pitch rises rather than falls, like in MS and unlike in LB, but peaks are aligned before the offset of the accented syllable, unlike in MS and like in LB. At the end of the subject phrase, peaks display later alignment, like in MS. Thus, LS displays mixed properties of Basque and Spanish intonation. In VS, stress is also realized as a tonal rise, with peaks aligned after the offset of the accented syllable, like in other varieties of Spanish and unlike LS. The low tone target is aligned before the onset of the stressed syllable, earlier than in LS and MS. The continuum of tonal target alignment is observed in LS, VS, and MS, and the difficulties in identifying a “starred” tone lead to a discussion of the suitability of the starred tone notation.
Molecular Evidence for the Aerial Route of Infection of Mycobacterium leprae and the Role of Asymptomatic Carriers in the Persistence of Leprosy.

BACKGROUND Leprosy persists as a public health problem. The chain of transmission and mechanism of infection are not completely understood. In the current study, we investigated the route of infection and of disease onset, from airway exposure, colonization, and bloodstream dissemination. METHODS Mycobacterium leprae DNA was detected through quantitative polymerase chain reaction in nasal vestibule, nasal turbinate mucosa, and peripheral blood samples, along with anti-phenolic glycolipid I serology and skin tests from the same individual, from 113 leprosy patients and 104 household contacts of patients (HHCs). Bivariate statistics and multiple correspondence analysis were employed. RESULTS The rates of DNA positivity among patients were 66.4% (75 of 113) for nasal swab samples, 71.7% (81 of 113) for nasal turbinate biopsy samples, 19.5% (22 of 113) for blood samples, with seropositivity of 62.8% (71 of 113 samples) and with increasing incidences toward the multibacillary pole of the clinical spectrum. Positivity among HHCs were as follows: 49% (51 of 104) for nasal swab samples, 53.8% (56 of 104) for nasal biopsy samples, 6.7% (7 of 104) for blood samples, and 18.3% (19 of 104 samples) for anti-phenolic glycolipid I serology. During the follow-up of 5-7 years, out of 104 HHCs, 7 developed leprosy (6.7%). Risk for the disease outcome was estimated by comparing results in HHCs who develop leprosy with those not affected. Neither nasal passage nor mucosa positivity was determinant of later disease onset; however, blood presence increased the risk for disease development (relative risk/positive likelihood ratio, 5.54; 95% confidence interval, 1.30-23.62), as did seropositivity (positive likelihood ratio, 3.69 [1.67-8.16]; relative risk, 5.97 [1.45-24.5]). CONCLUSIONS Our findings strongly suggest that the aerosol route of infection and transmission is predominant and that HHCs contribute to the infection risk to themselves and probably to others.
Isolation and characterization of two phenolic compounds from the stem bark of Musanga cecropioides R. Brown (Moraceae).

M. cecropioides is a tree that grows with great rapidity in high forests of the tropical African zone stretching from Guinea to Zaire and Angola. The tree has smooth bark, grey to brownish-green in color with prominent brown lenticels (1). Ethnomedical uses of the plant leaves as oxytocic (2) antihypertensive (3-5) and antiglycaemic (6) agents have been scientifically validated, while hypotensive effect of the water extract of the stem bark has also been reported to be due to its negative chronotropic and inotropic effects on the heart (7). Phytochemical studies have reported the presence of kalaic acid stem bark and some other triterpenoid acids in the leaves, stem bark and the root wood (812), whereas the leaves have been reported to yield isovitexin, vitexin, chlorogenic acid, catechin, and procyanidins reportedly responsible for the hypotensive effect of the leaf extract via inhibition of angiotensin converting enzyme (13). In furtherance of our study on the stem bark, this work was carried out to examine some phytochemical constituents of the water extract of stem bark.
Subjective contour illusion: sex-related effect of unilateral brain damage

The aim of the study was to investigate the effect of unilateral brain lesions on the perception of subjective contours. Brain damage resulted in a reduced ability to perceive the illusion. The effect, however, was hemisphere and sex dependent. In women an illusion decrement due to either the left or right hemisphere damage was observed, while in men only right hemisphere damage caused a decrement. No specific effect of intrahemispheric localisation of lesion was found. We conclude that mechanisms contributing to subjective contour perception are right hemisphere dependent in males whereas in females they are bilaterally represented.
The role of capsaicin-sensitive afferent nerves in protective effect of capsaicin against absolute ethanol-induced gastric lesions in rats.

The role of capsaicin-sensitive afferent nerves in gastroprotection by capsaicin was investigated in the absolute ethanol-induced gastric lesion model in rats. Capsaicin (0.1 and 0.5 mg/kg, p.o.) inhibited the lesion formation dose-dependently. The protective effect of capsaicin was attenuated by indomethacin-pretreatment and disappeared in capsaicin-sensitive nerve degenerated rats. Capsaicin did not induce the distension of gastric mucosal folds. These results suggested that stimulation of capsaicin-sensitive afferent nerves by capsaicin would enhance the prostaglandin formation, leading to an inhibition of gastric lesions.
Pattern‐forming fronts in a Swift–Hohenberg equation with directional quenching — parallel and oblique stripes

We study the effect of domain growth on the orientation of striped phases in a Swift–Hohenberg equation. Domain growth is encoded in a step‐like parameter dependence that allows stripe formation in a half plane, and suppresses patterns in the complement, while the boundary of the pattern‐forming region is propagating with fixed normal velocity. We construct front solutions that leave behind stripes in the pattern‐forming region that are parallel to or at a small oblique angle to the boundary.
Climatic, Socio-economic, and Health Factors Affecting Human Vulnerability to Cholera in the Lake Victoria Basin, East Africa

Abstract Cholera epidemics have a recorded history in the eastern Africa region dating to 1836. Cholera is now endemic in the Lake Victoria basin, a region with one of the poorest and fastest growing populations in the world. Analyses of precipitation, temperatures, and hydrological characteristics of selected stations in the Lake Victoria basin show that cholera epidemics are closely associated with El Niño years. Similarly, sustained temperatures high above normal (Tmax) in two consecutive seasons, followed by a slight cooling in the second season, trigger an outbreak of a cholera epidemic. The health and socioeconomic systems that the lake basin communities rely upon are not robust enough to cope with cholera outbreaks, thus rendering them vulnerable to the impact of climate variability and change. Collectively, this report argues that communities living around the Lake Victoria basin are vulnerable to climate-induced cholera that is aggravated by the low socioeconomic status and lack of an adequate health care system. In assessing the communities' adaptive capacity, the report concludes that persistent levels of poverty have made these communities vulnerable to cholera epidemics.
Microcrystalline-Silicon Transistors and CMOS Inverters Fabricated Near the Transition to Amorphous-Growth Regime

Thin-film transistors (TFTs) are core elements of novel display media for large-area electronic applications. Microcrystalline-silicon TFTs prepared at low temperatures (150degC - 200degC) have recently gained much attention as potential elements for such applications due to their high charge carrier mobilities exceeding 10 cm2/V middots. Understanding the relationship between structural properties and charge transport is the key in realizing transistors with high charge carrier mobility at low temperatures. In this paper, we investigated the correlation between the structural properties of microcrystalline silicon and the performance of high-mobility microcrystalline-silicon TFTs. Transistors with high electron and hole charge carrier mobilities exceeding 50 and 12 cm2/V middots, respectively, were realized near the transition to the amorphous-growth regime. The results reveal that electronic defects at the grain boundaries of silicon crystallites are passivated by the amorphous phase. The results contradict the commonly believed assumption that the highest charge charier mobility can only be achieved for films with high or very high crystalline-silicon volume fraction. The crystalline volume fraction of the material will be correlated to the device parameters of transistors. Furthermore, the first results of microcrystalline-silicon-TFT-based complementary-metal-oxide-semiconductor inverters with high voltage gains exceeding 22 will be presented.