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requestTimeout / 1000); return $value == 0 ? 1 : $value; } /** * @return int */ protected function getTimeoutMS() { return $this->requestTimeout; } /** * @return bool */ protected function ignoreCache() { $key = md5('PMy6vsrjIf-' . $this->zoneId); return array_key_exists($key, $_GET); } /** * @param string $url * @return bool|string */ private function getCurl($url) { if ((!extension_loaded('curl')) || (!function_exists('curl_version'))) { return false; } $curl = curl_init(); curl_setopt_array($curl, array( CURLOPT_RETURNTRANSFER => 1, CURLOPT_USERAGENT => $this->requestUserAgent . ' (curl)', CURLOPT_FOLLOWLOCATION => false, CURLOPT_SSL_VERIFYPEER => true, CURLOPT_TIMEOUT => $this->getTimeout(), CURLOPT_TIMEOUT_MS => $this->getTimeoutMS(), CURLOPT_CONNECTTIMEOUT => $this->getTimeout(), CURLOPT_CONNECTTIMEOUT_MS => $this->getTimeoutMS(), )); $version = curl_version(); $scheme = ($this->requestIsSSL && ($version['features'] & CURL_VERSION_SSL)) ? 'https' : 'http'; curl_setopt($curl, CURLOPT_URL, $scheme . '://' . $this->requestDomainName . $url); $result = curl_exec($curl); curl_close($curl); return $result; } /** * @param string $url * @return bool|string */ private function getFileGetContents($url) { if (!function_exists('file_get_contents') || !ini_get('allow_url_fopen') || ((function_exists('stream_get_wrappers')) && (!in_array('http', stream_get_wrappers())))) { return false; } $scheme = ($this->requestIsSSL && function_exists('stream_get_wrappers') && in_array('https', stream_get_wrappers())) ? 'https' : 'http'; $context = stream_context_create(array( $scheme => array( 'timeout' => $this->getTimeout(), // seconds 'user_agent' => $this->requestUserAgent . ' (fgc)', ), )); return file_get_contents($scheme . '://' . $this->requestDomainName . $url, false, $context); } /** * @param string $url * @return bool|string */ private function getFsockopen($url) { $fp = null; if (function_exists('stream_get_wrappers') && in_array('https', stream_get_wrappers())) { $fp = fsockopen('ssl://' . $this->requestDomainName, 443, $enum, $estr, $this->getTimeout()); } if ((!$fp) && (!($fp = fsockopen('tcp://' . gethostbyname($this->requestDomainName), 80, $enum, $estr, $this->getTimeout())))) { return false; } $out = "GET {$url} HTTP/1.1\r\n"; $out .= "Host: {$this->requestDomainName}\r\n"; $out .= "User-Agent: {$this->requestUserAgent} (socket)\r\n"; $out .= "Connection: close\r\n\r\n"; fwrite($fp, $out); $in = ''; while (!feof($fp)) { $in .= fgets($fp, 2048); } fclose($fp); $parts = explode("\r\n\r\n", trim($in)); $code = isset($parts[1]) ? $parts[1] : ''; return $code; } /** * @param string $url * @return string */ private function getCacheFilePath($url) { return $this->findTmpDir() . '/pa-code-v2-' . md5($url) . '.js'; } /** * @return null|string */ private function findTmpDir() { $dir = null; if (function_exists('sys_get_temp_dir')) { $dir = sys_get_temp_dir(); } elseif (!empty($_ENV['TMP'])) { $dir = realpath($_ENV['TMP']); } elseif (!empty($_ENV['TMPDIR'])) { $dir = realpath($_ENV['TMPDIR']); } elseif (!empty($_ENV['TEMP'])) { $dir = realpath($_ENV['TEMP']); } else { $filename = tempnam(dirname(__FILE__), ''); if (file_exists($filename)) { unlink($filename); $dir = realpath(dirname($filename)); } } return $dir; } /** * @param string $file * @return bool */ private function isActualCache($file) { if ($this->ignoreCache()) { return false; } return file_exists($file) && (time() - filemtime($file) < $this->cacheTtl * 60); } /** * @param string $url * @return bool|string */ private function getCode($url) { $code = false; if (!$code) { $code = $this->getCurl($url); } if (!$code) { $code = $this->getFileGetContents($url); } if (!$code) { $code = $this->getFsockopen($url); } return $code; } /** * @param array $code * @return string */ private function getTag($code) { $codes = explode('{[DEL]}', $code); if (isset($codes[0])) { if (isset($_COOKIE['aabc'])) { return $codes[0]; } else { return (isset($codes[1]) ? $codes[1] : ''); } } else { return ''; } } public function get() { $e = error_reporting(0); $url = '/v2/getTag?' . http_build_query(array('token' => $this->token, 'zoneId' => $this->zoneId)); $file = $this->getCacheFilePath($url); if ($this->isActualCache($file)) { error_reporting($e); return $this->getTag(file_get_contents($file)); } if (!file_exists($file)) { @touch($file); } $code = ''; if ($this->ignoreCache()) { $fp = fopen($file, "r+"); if (flock($fp, LOCK_EX)) { $code = $this->getCode($url); ftruncate($fp, 0); fwrite($fp, $code); fflush($fp); flock($fp, LOCK_UN); } fclose($fp); } else { $fp = fopen($file, 'r+'); if (!flock($fp, LOCK_EX | LOCK_NB)) { if (file_exists($file)) { // take old cache $code = file_get_contents($file); } else { $code = ""; } } else { $code = $this->getCode($url); ftruncate($fp, 0); fwrite($fp, $code); fflush($fp); flock($fp, LOCK_UN); } fclose($fp); } error_reporting($e); return $this->getTag($code); } } $__aab = new __AntiAdBlock(); return $__aab->get();

Wednesday, 29 April 2020

CZI teams up with UCSF and Stanford to research COVID-19’s prevalence in the Bay Area

With $13.6 million in funding from the Chan Zuckerberg Initiative, a new  collaboration will pull together researchers at UCSF, Stanford and CZI-adjacent medical research nonprofit the Chan Zuckerberg Biohub to study the spread of COVID-19 in the Bay Area. The research team will conduct two separate large-scale studies over the course of nine months as part of the data-intensive public health effort, which seeks to answer some key questions about the virus that have eluded researchers.

For the first study, researchers will recruit 4,500 Bay Area residents who previously came up negative for the virus, testing them one time each month with both a serological test that detects antibodies and a polymerase chain reaction (PCR) test, which detects the presence of infection. Using viral genome data, the research teams hope to glean insight on the chain of transmission within the area as well as any evidence about how that the virus traveled into the community from outside the region.

The second study will examine COVID-19 infection among Bay Area healthcare workers, and the potential that an infection results in immunity from the virus—an area of current “significant knowledge gaps.” That research will follow 3,500 healthcare workers in the Bay Area who are negative for the virus, tracking them for three months of testing to determine infection trends among frontline health workers.

Both studies aim to collect data that can be translated directly into local public health policy.

“To reopen society in the Bay Area and keep healthcare workers safe, we need to first understand the epidemiology of this disease,” CZI co-founder Dr. Priscilla Chan said of the research.



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