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2018 年 09 月 28 日

DragonFly BSD Digest

BSDNow 265: Software Disenchantment

BSDNow 265 has a con report – the just-finished EuroBSDCon 2018 in Romania, plus the usual roundup of news items.  One news item that will be useful someday: how to perform a BIOS update on a non-Windows computer.

by Justin Sherrill at 2018-09-28, 02:22 上午

2018 年 09 月 27 日



It used to happen sporadically but now it is a daily experience. As I am browsing the net I click on a link (usually a newspaper website). The page starts to load. Then I wait. And I wait. And I wait. It takes several seconds. Once loaded, my patience is not rewarded since my MacBook Air mid-2011 seems to barely be able to keep up. Videos start playing left and right. Sound is not even turned off by default anymore. This shitshow festival of lights and sounds is discouraging but I am committed to learn about world news. I continue. I have the silly idea to scroll down (searching for the meaty citations located between double quotes) and the framerate drops to 15 frames per second. Later, for no apparent reason, all fans will start running at full speed. The air exhaust will expel burning hot air. MacOS X's ActivityMonitor.app reveals countless "Helpers" processes which are not helping at all. I wonder if the machine is going to die on my lap, or take off like a jet and fly away.

This happens even on my brand new laptop or my crazy powerful custom PC. This short article is basically a reply to the article we talked about earlier this week, and I'm pretty sure this is a subject we won't be done with for a long time to come.

by donotreply@osnews.com (Thom Holwerda) at 2018-09-27, 10:36 下午

Meet the community keeping obsolete supercomputers alive

Nearly 30 years after Silicon Graphics ruled the high-performance computing roost, its supercomputers have found themselves a new home with a small community full of enthusiasts - some of whom weren&apost even alive during the company's heyday.

SGI machines are definitely on my list of platforms to sink my teeth into in the future. I don't think I'll be focusing on these more eccentric supercomputer-type workstations, but they are fascinating nonetheless. I'm very glad there's an active community of people keeping these machines working.

by donotreply@osnews.com (Thom Holwerda) at 2018-09-27, 10:18 下午

Killing processes that don't want to die

Suppose you have a program running on your system that you don't quite trust. Maybe it's a program submitted by a student to an automated grading system. Or maybe it's a QEMU device model running in a Xen control domain ("domain 0" or "dom0"), and you want to make sure that even if an attacker from a rogue virtual machine manages to take over the QEMU process, they can't do any further harm. There are many things you want to do as far as restricting its ability to do mischief. But one thing in particular you probably want to do is to be able to reliably kill the process once you think it should be done. This turns out to be quite a bit more tricky than you'd think.

by donotreply@osnews.com (Thom Holwerda) at 2018-09-27, 07:05 下午

Qualcomm accuses Apple of stealing chip secrets

I've been away for a few days, so there's some backlog for me to chew through.

Qualcomm has unveiled explosive charges against Apple, accusing it of stealing "vast swaths" of confidential information and trade secrets for the purpose of improving the performance of chips provided by rival Intel, according to a court filing. Qualcomm hopes the court will amend allegations in its existing lawsuit against Apple accusing it of breaching the so called master software agreement that Apple signed when it became a customer of Qualcomm's earlier this decade.

One unlikeable horrible company fighting the other. Am I supposed to root for someone here?

by donotreply@osnews.com (Thom Holwerda) at 2018-09-27, 07:04 下午

ScienceNOW daily headlines

Ancient lowland Maya complexity as revealed by airborne laser scanning of northern Guatemala

Lowland Maya civilization flourished in the tropical region of the Yucatan peninsula and environs for more than 2500 years (~1000 BCE to 1500 CE). Known for its sophistication in writing, art, architecture, astronomy, and mathematics, Maya civilization still poses questions about the nature of its cities and surrounding populations because of its location in an inaccessible forest. In 2016, an aerial lidar survey across 2144 square kilometers of northern Guatemala mapped natural terrain and archaeological features over several distinct areas. We present results from these data, revealing interconnected urban settlement and landscapes with extensive infrastructural development. Studied through a joint international effort of interdisciplinary teams sharing protocols, this lidar survey compels a reevaluation of Maya demography, agriculture, and political economy and suggests future avenues of field research.

by Canuto, M. A., Estrada-Belli, F., Garrison, T. G., Houston, S. D., Acuna, M. J., Kovac, M., Marken, D., Nondedeo, P., Auld-Thomas, L., Castanet, C., Chatelain, D., Chiriboga, C. R., Drapela, T., Lieskovsky, T., Tokovinine, A., Velasquez, A., Fernandez-Diaz, J. C., Shrestha, R. at 2018-09-27, 05:39 下午

Response to Comment on "DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification"

Following the Comment of Stewart et al., we repeated our analysis on sequencing runs from The Cancer Genome Atlas (TCGA) using their suggested parameters. We found signs of oxidative damage in all sequence contexts and irrespective of the sequencing date, reaffirming that DNA damage affects mutation-calling pipelines in their ability to accurately identify somatic variations.

by Chen, L., Liu, P., Evans, T. C., Ettwiller, L. M. at 2018-09-27, 05:39 下午

Comment on "The plateau of human mortality: Demography of longevity pioneers"

Barbi et al. (Reports, 29 June 2018, p. 1459) reported that human mortality rate reached a "plateau" after the age of 105, suggesting there may be no limit to human longevity. We show, using their data, that potential lifespans cannot increase much beyond the current 122 years unless future biomedical advances alter the intrinsic rate of human aging.

by Beltran-Sanchez, H., Austad, S. N., Finch, C. E. at 2018-09-27, 05:39 下午

Chromatin plasticity: A versatile landscape that underlies cell fate and identity

During development and throughout life, a variety of specialized cells must be generated to ensure the proper function of each tissue and organ. Chromatin plays a key role in determining cellular state, whether totipotent, pluripotent, multipotent, or differentiated. We highlight chromatin dynamics involved in the generation of pluripotent stem cells as well as their influence on cell fate decision and reprogramming. We focus on the capacity of histone variants, chaperones, modifications, and heterochromatin factors to influence cell identity and its plasticity. Recent technological advances have provided tools to elucidate the underlying chromatin dynamics for a better understanding of normal development and pathological conditions, with avenues for potential therapeutic application.

by Yadav, T., Quivy, J.-P., Almouzni, G. at 2018-09-27, 05:39 下午

Dynamic DNA methylation: In the right place at the right time

The classical model of cytosine DNA methylation (the presence of 5-methylcytosine, 5mC) regulation depicts this covalent modification as a stable repressive regulator of promoter activity. However, whole-genome analysis of 5mC reveals widespread tissue- and cell type–specific patterns and pervasive dynamics during mammalian development. Here we review recent findings that delineate 5mC functions in developmental stages and diverse genomic compartments as well as discuss the molecular mechanisms that connect transcriptional regulation and 5mC. Beyond the newly appreciated dynamics, regulatory roles for 5mC have been suggested in new biological contexts, such as learning and memory or aging. The use of new single-cell measurement techniques and precise editing tools will enable functional analyses of 5mC in gene expression, clarifying its role in various biological processes.

by Luo, C., Hajkova, P., Ecker, J. R. at 2018-09-27, 05:39 下午

Developmental enhancers and chromosome topology

Developmental enhancers mediate on/off patterns of gene expression in specific cell types at particular stages during metazoan embryogenesis. They typically integrate multiple signals and regulatory determinants to achieve precise spatiotemporal expression. Such enhancers can map quite far—one megabase or more—from the genes they regulate. How remote enhancers relay regulatory information to their target promoters is one of the central mysteries of genome organization and function. A variety of contrasting mechanisms have been proposed over the years, including enhancer tracking, linking, looping, and mobilization to transcription factories. We argue that extreme versions of these mechanisms cannot account for the transcriptional dynamics and precision seen in living cells, tissues, and embryos. We describe emerging evidence for dynamic three-dimensional hubs that combine different elements of the classical models.

by Furlong, E. E. M., Levine, M. at 2018-09-27, 05:39 下午

RNA modifications modulate gene expression during development

RNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programs. They affect diverse eukaryotic biological processes, and the correct deposition of many of these modifications is required for normal development. Messenger RNA (mRNA) modifications regulate various aspects of mRNA metabolism. For example, N6-methyladenosine (m6A) affects the translation and stability of the modified transcripts, thus providing a mechanism to coordinate the regulation of groups of transcripts during cell state maintenance and transition. Similarly, some modifications in transfer RNAs are essential for RNA structure and function. Others are deposited in response to external cues and adapt global protein synthesis and gene-specific translational accordingly and thereby facilitate proper development.

by Frye, M., Harada, B. T., Behm, M., He, C. at 2018-09-27, 05:39 下午

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Last updated: 2018-09-28, 03:45 上午