Letter from C.L. W[aterston] to [Jeanne C.] Carr, 1871 Jul 10.

71 Chester Square, Boston,July 10, 1871.Dear Mrs. Carr,On my return a few days ago from a journey I found a letter directed by you, and containing two letters from Mr. Muir to yourself. I searched in vain for any word from yourself, and as the letter was postmarked \u27Boston\u27 I presume you gave them hurriedly to some friend on his way here. I thank you much for the privilege of reading these letters -- they are poems of great and exquisite beauty -- worthy to be written out of a heart whose close communion with nature springs to a perfect love. \u27Too near to God for doubt or fear,He shares the eternal calm\u27.It is delightful to me to know that there is such a soul among those wonderful sky ceiled rocks , amid those great visions, the great white throne of the Central Dome. I feel His glory who could make a world,Yet in the lost depth of the wildernessLeave not a flower unfinished .What rest, what perfect trust, we ought to feel in such a Father of Nature, Soul and Spirit.I trust such healing wings have closed around your wounded spirit and carried you up to the serene heights of Peace. You can hardly resist the call to the Yosemite. How I wish I could join you there, with Mr. Muir for a guide. I am glad he met Mr. Emerson. I only wonder how Mr. E. could resist camping out under the Great Trees.A year has passed since we were at the Yosemite -- a year -- it seems hardly a day. I have a picture of the Sentinel Rock, hanging opposite my room. It is by Mr. Shapleigh, who was in the Valley with us. I chose it from all his sketches, and call it my Rock. It is indeed the Rock which is higher than I, and typifies many things spiritual and eternal, while recalling the great original at whose foot we dwelt.I should like to keep Mr. Muir\u27s letters until I hear from you again, so do not enclose them -- they are safe and much prized.Mr. Waterston and I have just returned from a five weeks\u27 trip to the Green Mts., where we have enjoyed ourselves very highly. We spent a day or two to Brandon, but unfortunately Charlie Sanderson had not arrived at his cottage. We walked to it and looked in at the window and saw white muslin curtains, a print of Beethoven and other tokens of its master\u27s pure and peaceful soul. I slipped a card under the door and took a rosebud from a bush near it. A note from Perabo tells me he is just going to join C. S. there. I met Mrs. Mary Parkman this spring, and spoke to her of my having seen you in California. She did not know where you were residing. She desired me to give you her kind regards, and remembered with interest your kindness and regard for her husband. Mr. Waterston met Ole Bull one evening at a Club where he seemed very bright and happy -- the baby must seem like a grandchild to him, as indeed it should be.We returned for the closing exercises of the schools, as Mr. W. is on the committee and we have just entertained at our house the graduating class of the Everett School - 55 girls -- a rose garden of girls they looked in their white muslins. How does your University and various interests progress? Mr. W. had a very interesting letter from Mr. Bacon lately, who writes many pleasant things. I wish Oakland was not three thousand miles off!So they sentenced Mrs. Fair -- it was more than I expected. If anyone deserves capital punishment it would seem to be in such a case, and yet -- well, God knows how to deal with sinners better than we do.Mrs. Howison is out of town. I saw her bright face just before we all went away. Hoping to hear from you soon, we send many best loves. I go this week to Newport to stay with my sister, but our letters are sent here.Ever yours,C. L. W[aterston]4600408

Early post parturient changes in milk acute phase proteins

The periparturient period is one of the most critical periods in the productive life of a dairy cow, and is the period when dairy cows are most susceptible to developing new intramammary infections (IMI) leading to mastitis. Acute phase proteins (APP) such as haptoglobin (Hp), mammary associated serum amyloid A3 (M-SAA3) and C-reactive protein (CRP) have been detected in milk during mastitis but their presence in colostrum and milk in the immediate postpartum period has had limited investigation. The hypothesis was tested that APP are a constituent of colostrum and milk during this period. Enzyme linked immunosorbent assays (ELISAs) were used to determine each APP’s concentration in colostrum and milk collected daily from the first to tenth day following calving in 22 Holstein-Friesian dairy cows. Haptoglobin was assessed in individual quarters and composite milk samples while M-SAA3 and CRP concentration were determined in composite milk samples. Change in Hp in relation to the high abundance proteins during the transition from colostrum to milk were evaluated by 1 and 2 dimension electrophoresis and western blot. In 80% of the cows all APPs were detected in colostrum on the first day following parturition at moderately high levels but gradually decreased to minimal values in the milk by the 6th day after calving. The remaining cows (20%) showed different patterns in the daily milk APP concentrations and when an elevated level is detected could reflect the presence of IMI. Demonstration that APP are present in colostrum and milk following parturition but fall to low levels within 4 days means that elevated APP after this time could be biomarkers of post parturient mastitis allowing early intervention to reduce disease on dairy farms

Effect of pre-analytical treatments on bovine milk acute phase proteins

Background Samples for diagnostic procedures often require some form of pre-analytical preparation for preservation or safe handling during transportation prior to analysis in the laboratory. This is particularly important for milk samples which frequently need preservatives to retain milk composition as close to that found in freshly collected samples as possible. Methods Milk samples were treated by heating at 56 °C for 30 min or preserved by addition of either potassium dichromate or bronopol respectively. Haptoglobin (Hp), mammary associated serum amyloid A3 (M-SAA3) and C-reactive protein (CRP) were measured in the various treatment groups and in control samples which were not treated, using enzyme linked immunoassays. The concentrations of each APP were compared between treated and non-treated groups using the Wilcoxon signed ranks tests. Results Heat treatment of samples was found to have a significant lowering effect on milk M-SAA3 and CRP but not Hp. The use of potassium dichromate and bronopol as preservatives in milk had no significant effects on milk Hp and M-SAA3 concentration but lowered milk CRP values compared to controls. Conclusions The observed effects of heating and preservative use on milk APP should be taken into consideration when assaying samples which have undergone heat treatment as a result of international transfer regulations involving biological samples or samples needing chemical preservation prior to transport to laboratory

Spectral Analysis of Guanine and Cytosine Fluctuations of Mouse Genomic DNA

We study global fluctuations of the guanine and cytosine base content (GC%) in mouse genomic DNA using spectral analyses. Power spectra S(f) of GC% fluctuations in all nineteen autosomal and two sex chromosomes are observed to have the universal functional form S(f) \sim 1/f^alpha (alpha \approx 1) over several orders of magnitude in the frequency range 10^-7< f < 10^-5 cycle/base, corresponding to long-ranging GC% correlations at distances between 100 kb and 10 Mb. S(f) for higher frequencies (f > 10^-5 cycle/base) shows a flattened power-law function with alpha < 1 across all twenty-one chromosomes. The substitution of about 38% interspersed repeats does not affect the functional form of S(f), indicating that these are not predominantly responsible for the long-ranged multi-scale GC% fluctuations in mammalian genomes. Several biological implications of the large-scale GC% fluctuation are discussed, including neutral evolutionary history by DNA duplication, chromosomal bands, spatial distribution of transcription units (genes), replication timing, and recombination hot spots.Comment: 15 pages (figures included), 2 figure

Acute phase protein response in an experimental model of ovine caseous lymphadenitis

<p>Abstract</p> <p>Background</p> <p>Caseous lymphadenitis (CLA) is a disease of small ruminants caused by <it>Corynebacterium pseudotuberculosis</it>. The pathogenesis of CLA is a slow process, and produces a chronic rather than an acute disease state. Acute phase proteins (APP) such as haptoglobin (Hp) serum amyloid A (SAA) and α₁acid glycoprotein (AGP) are produced by the liver and released into the circulation in response to pro-inflammatory cytokines. The concentration of Hp in serum increases in experimental CLA but it is not known if SAA and AGP respond in parallel or have differing response profiles.</p> <p>Results</p> <p>The concentration in serum of Hp, SAA and AGP in 6 sheep challenged with 2 × 10⁵cells of <it>C. pseudotuberculosis </it>showed significant increases (P < 0.05) compared to 3 unchallenged control sheep. By day 7 post infection. (p.i.) the Hp and SAA concentrations reached mean (± SEM) values of 1.65 ± 0.21 g/L and 18.1 ± 5.2 mg/L respectively. Thereafter, their concentrations fell with no significant difference to those of the control sheep by day 18 p.i.. In contrast, the serum AGP concentration in infected sheep continued to rise to a peak of 0.38 ± 0.05 g/L on day 13 p.i., after which a slow decline occurred, although the mean concentration remained significantly higher (P < 0.05) than the control group up to 29 days p.i.. Specific IgG to phospholidase D of <it>C. pseudotuberculosis </it>became detectable at 11 days p.i. and continued to rise throughout the experiment.</p> <p>Conclusion</p> <p>The serum concentrations of Hp, SAA and AGP were raised in sheep in an experimental model of CLA. An extended response was found for AGP which occurred at a point when the infection was likely to have been transforming from an acute to a chronic phase. The results suggest that AGP could have a role as a marker for chronic conditions in sheep.</p

The pre treatment systemic inflammatory response is an important determinant of poor pathologic response for patients undergoing neoadjuvant therapy for rectal cancer

Background Not all patients respond equally to neoadjuvant chemoradiotherapy (nCRT), with subsequent effects on survival. The systemic inflammatory response has been shown to predict long-term outcomes in colorectal cancer. The current study examined the association between systemic inflammation and nCRT in patients with rectal cancer. Methods Between 1999 and 2010, patients who underwent nCRT were identified. Serum measurements of hemoglobin, C-reactive protein, albumin, modified Glasgow prognostic score (mGPS), and differential white cell counts were obtained before and after nCRT. The Rödel scoring system measured pathologic tumor regression, and magnetic resonance imaging and computed tomography determined radiologic staging. Results The study included 79 patients. Of these patients, 37% were radiologically downstaged, and 44% were categorized as showing a good pathologic response (Rödel scores 3 and 4). As a validated measure of the systemic inflammatory response, mGPS (P = 0.022) was associated with a poor pathologic response to nCRT. A radiologic response was associated with a good pathologic response to treatment (P = 0.003). A binary logistic regression model identified mGPS (odds ratio [OR] 0.27; 95% confidence interval [CI] 0.07–0.96; P = 0.043) and radiologic response (OR 0.43; 95% CI 0.18–0.99; P = 0.048) as strong independent predictors of a pathologic response to treatment. Conclusion The current study showed that a systemic inflammatory response before nCRT is associated with a poor pathologic response. Further study in a prospective controlled trial setting is warranted. Stephan B. Dreyer and Arfon G. M. T. Powell—contributed equally. Colorectal cancer (CRC) is the third most common cancer and the second highest cause of cancer death in the United Kingdom.1 The 5-year survival rate for CRC still is less than 60% with surgery alone, offering the only chance of cure. Rectal cancers comprise about one third of surgical resections for colorectal cancer.2 The widely adapted surgical technique of total mesorectal excision (TME), increased centralization, specialization of rectal surgery, and earlier disease detection have led to improved survival in the last 30 years.3,4 Preoperative neoadjuvant radiotherapy with or without chemotherapy currently is accepted as a standard of care for patients with margin-threatening rectal cancer. This increases disease-free survival (DFS) and sphincter preservation rates and improves circumferential resection margins and local recurrence rates.5–8 Current management of CRC in the United Kingdom involves evaluating patients using magnetic resonance imaging (MRI) and computed tomography (CT) before treatment to identify those with margin-threatening disease (T3 or T4).9 These patients are offered neoadjuvant chemoradiotherapy (nCRT) before surgical resection.10 Not all patients respond to nCRT, and there is a need to identify biomarkers of response because treatment is associated with significant morbidity. Rödel et al.11 have shown that the presence of spontaneous apoptosis in the resected specimen is a good marker of tumor regression and improved prognosis. The prognostic value of the systemic inflammatory response (SIR) has been widely studied in gastrointestinal cancers, particularly in the operative setting, using measurements of circulating markers including C-reactive protein (CRP), albumin, the modified Glasgow prognostic score (mGPS), the neutrophil lympocyte ratio (NLR), the platelet-to-lymphocyte ratio (PLR), and more recently, the neutrophil-platelet score (NPS) and the derived neutrophil-to-lymphocyte ratio (dNLR).12–16 This study investigated the association between markers of the systemic inflammatory response and the pathologic response to nCRT in patients with rectal cancer

Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species

BACKGROUND: Codon usage has direct utility in molecular characterization of species and is also a marker for molecular evolution. To understand codon usage within the diverse phylum Nematoda, we analyzed a total of 265,494 expressed sequence tags (ESTs) from 30 nematode species. The full genomes of Caenorhabditis elegans and C. briggsae were also examined. A total of 25,871,325 codons were analyzed and a comprehensive codon usage table for all species was generated. This is the first codon usage table available for 24 of these organisms. RESULTS: Codon usage similarity in Nematoda usually persists over the breadth of a genus but then rapidly diminishes even within each clade. Globodera, Meloidogyne, Pristionchus, and Strongyloides have the most highly derived patterns of codon usage. The major factor affecting differences in codon usage between species is the coding sequence GC content, which varies in nematodes from 32% to 51%. Coding GC content (measured as GC3) also explains much of the observed variation in the effective number of codons (R = 0.70), which is a measure of codon bias, and it even accounts for differences in amino acid frequency. Codon usage is also affected by neighboring nucleotides (N1 context). Coding GC content correlates strongly with estimated noncoding genomic GC content (R = 0.92). On examining abundant clusters in five species, candidate optimal codons were identified that may be preferred in highly expressed transcripts. CONCLUSION: Evolutionary models indicate that total genomic GC content, probably the product of directional mutation pressure, drives codon usage rather than the converse, a conclusion that is supported by examination of nematode genomes

Kaposi's sarcoma-associated herpesvirus oncoprotein K13 protects against B cell receptor induced growth arrest and apoptosis through NF-κB activation

Kaposi's sarcoma-associated herpesvirus (KSHV) has been linked to the development of Kaposi's sarcoma, primary effusion lymphoma and multicentric Castleman's disease (MCD). We have characterized the role of KSHV-encoded viral FLICE inhibitory protein K13 in the modulation of anti-IgM induced growth arrest and apoptosis in B cells. We demonstrate that K13 protects WEHI 231, an immature B cell line, against anti-IgM induced growth arrest and apoptosis. The protective effect of K13 was associated with the activation of the NF-κB pathway and was deficient in its mutant, K13-58AAA, and a structural homolog, vFLIP E8, which lack NF-κB activity. K13 upregulated the expression of NF-κB subunit RelB and blocked the anti-IgM induced decline in c-Myc and rise in p27(Kip1) that have been associated with growth arrest and apoptosis. K13 also upregulated the expression of Mcl-1, an anti-apoptotic member of the Bcl2 family. Finally, K13 protected the mature B cell line Ramos against anti-IgM induced apoptosis through NF-κB activation. Inhibition of anti-IgM induced apoptosis by K13 may contribute to the development of KSHV-associated lymphoproliferative disorders

Non-perturbative dynamics of hot non-Abelian gauge fields: beyond leading log approximation

Many aspects of high-temperature gauge theories, such as the electroweak baryon number violation rate, color conductivity, and the hard gluon damping rate, have previously been understood only at leading logarithmic order (that is, neglecting effects suppressed only by an inverse logarithm of the gauge coupling). We discuss how to systematically go beyond leading logarithmic order in the analysis of physical quantities. Specifically, we extend to next-to-leading-log order (NLLO) the simple leading-log effective theory due to Bodeker that describes non-perturbative color physics in hot non-Abelian plasmas. A suitable scaling analysis is used to show that no new operators enter the effective theory at next-to-leading-log order. However, a NLLO calculation of the color conductivity is required, and we report the resulting value. Our NLLO result for the color conductivity can be trivially combined with previous numerical work by G. Moore to yield a NLLO result for the hot electroweak baryon number violation rate.Comment: 20 pages, 1 figur

Bermuda 2.0: Reflections from Santa Cruz

In February 1996, the genome community met in Bermuda to formulate principles for circulating genomic data. Although it is now 20 years since the Bermuda Principles were formulated, they continue to play a central role in shaping genomic and data-sharing practices. However, since 1996, “openness” has become an increasingly complex issue. This commentary seeks to articulate three core challenges data-sharing faces today