OpenLLM-France/wikimedia huggingface dataset:
# Structural Biochemistry/Bioinformatics/Protein Fold Recognition
## Overview

One of the biggest problems in bioinformatics is the relationship between amino acid sequence, structure, and function of proteins. The three dimensional structure of proteins helps in the development of drugs, engineering of enzymes, and analysis of protein functions.
There is the much-debated controversy of structural space and the conservation of structures and their relationship to the homology of proteins. The prediction of tertiary structures, however, relies on the re-use of subjective fragments without the need for homologous sequences (between target sequence and fragment source).
One of the many methods used by biologists and researchers to predict the tertiary structure of proteins is the GenTHREADER. This method aids in the detection of protein templates and sequence-structure alignment accuracy. Most methods used for fold prediction use known protein structures as a basis of the scoring of alignments calculated among protein sequence profiles. Two versions of GenTHREADER are the pGenTHREADER and pDomTHREADER methods, which are used to recognize and align protein sequences in order to analyze their relationship to the structure and function of the protein. Both of these versions have similar inputs of protein sequence profiles and structural information; the use one core alignment algorithm.
The pGenTHREADER uses profile-profile comparisons from matrices built from sequences, coiled coil regions and filtered trans-membrane fragments. The final step includes two sequence-profile and profile-sequence scores, which enabled profile-profile matches that was higher scoring that other matches. In addition, a hydrophobic burial terms is added that serves the purpose of biasing alignments’ positions in a target sequence.
In determining results, the best results of a template-target pair were used to calculate the number of equivalent residues rather than the results for a method; this differentiates alignment accuracy from template selection. Picking the best result significantly improves performance of chains less than 200 amino acids but shows little improvements in longer chains. pGenTHREADER works significantly better than other methods when the fold recognition relationships are more distant; with shorter distances, other methods tend to show more improvement. These other methods used mixes of fold recognition, side chain optimizations and model quality assessments.
# US Criminal Law/Actus reus

* Actus Reus (Latin for "guilty act") is the physical aspect of the crime. It can be an act or a failure to act where the person is required to act (e.g. a parent failing to protect their child). For example, the actus reus of battery is the physical contact between the assailant and victim (except that simple battery (without intent to do a further crime) is a tort, not a crime, and should not be confused).
* Another example would be theft. The crime of theft requires physically taking something away (the actus reus) along with the intent to deprive the owner of the property indefinitely (the mens rea).
* Q. Which of the following aspect of actus reus is not required?
* causation
* voluntariness
* intention
* physical capability
* Q. Which of the following could potentially constitute an actus reus?
* Uploading spyware in order to harm your friend's computer
* Hurting someone in the dream
* An assassin with a plan to kill someone but failed to act on the plan
* Some special "act" such as possession can be actus reus. For example, possession of drugs is a serious crime in many countries around the world. If possession is deemed a crime, the act of possession always is conscious possession - you need to be aware of the fact that there is cocaine in your bag. So here comes the "voluntary" aspect. An act cannot satisfy the actus reus requirement unless it is voluntary.
* Q. Does an act of reflex or convulsion give rise to criminal liability?
* No. (It is not voluntary.)
* Q. Does an act performed during a state of unconsciousness meet the actus reus requirement?
* No. (It is not voluntary.)
* Q. How about acts performed under hypnosis?
* The court is split about this issue. The Model Penal Code considers conduct under hypnosis as involuntary. For example: Mike Bookie, while taking the Criminal Law final exam, is stricken by epileptic convulsions and strikes John Wikie in the face. Since he did not hit John voluntarily, he does not have criminal liability.
* Some acts are not actus reus because they are not physical.
* Thoughts, words, possession and status
* We cannot punish someone for mere thoughts of doing something harmful. For instance, I write here, "I intend to burn all the WikiBooks." This does not constitute arson nor any crime.
* Causation
* Two main types of causation exist, therefore two tests are applied:
* Was the criminal act foreseeable?
* But for the act of someone else, the criminal act would not have occurred.
# US Criminal Law/Defenses/Insanity defense

The insanity defense is a rarely used legal argument. It is based upon the claim the defendant is suffering from a mental illness or mental incapacity. Under one of the rules for determining insanity, the M'Naghten rule, the defendant is considered not guilty if at the time of the crime the person did not know what he was doing or did not know what he was doing was wrong. While there are several other rules for determining insanity all of them focus upon the person not being fully aware of what they were doing or that the action was wrong because of a mental illness. If the person is found not guilty by reason of insanity the judge may order the person to be committed for psychiatric treatment until they are cured.
# US Criminal Law/Defenses/Prosecutorial misconduct

Prosecutorial misconduct can come in various forms, but it most commonly arises in a few ways. First, a prosecutor's sidebar statements during trial can be prosecutorial misconduct. These may be comments about the defendant, his attorney, a witness, or the judge. These comments can result in a mistrial with Pre-Judice (barring reprosecution), assuming the trial court concludes that they were made for the purpose of inciting the motion for mistrial. Other times, they will just result in a mistrial without prejudice. Second, a prosecutor's failure to turn over material, exculpatory evidence to the defense, in dereliction of his duties under Brady v. Maryland, 373 U.S. 83 (1963). This is a type of prosecutorial misconduct which may be raised at virtually any time, even post-conviction, as it is a constitutional error of great magnitude. If the defendant can prove the prosecutor failed to turn over Brady material, he will typically receive a new trial. Third, a prosecutor's selective prosecution of a person or group of people may be misconduct. Also, if a prosecutor increases the punishment or charges based on the defendant's exercise of his rights (to jury trial, of appeal, etc.), this may (under certain circumstances) be misconduct.
# US Criminal Law/Defenses

* There are four main types of legal defenses. They are Alibi, Justifications, Excuses and Procedural.
* Alibi
* When a defendant uses an argument based upon an alibi they are not only saying they are not guilty, but they are claiming to be innocent. The alibi is based upon the idea that they could not have committed that crime because they were elsewhere when the crime was committed. Typically in a criminal trial, the defense will attempt to assert proof of an alibi. Such proof can come from documentation of the defendant's whereabouts or testimony of someone who was with the defendant at the relevant time.
* In law school, this is commonly called the "SODDI" defense..."Some Other Dude Did It". Lawyers call it "alibi."
* Justification
* Justification defense requires the defendant to admit they committed the crime, but they are not guilty because committing the crime was the lesser of two evils. Self defense is the best known of this type of defense.
* Consent
* Self defense
* Defense of others
* Defense of property
* Necessity
* Resisting unlawful arrest
* Excuse defenses
* The Excuse defenses are based on the idea that the person, while they did commit the crime and the action was not justified, did not have the control or state of mind at the time the crime was committed to be held legally responsible for the crime. Insanity is the best known of the excuse defenses. Also, mitigating circumstances can lead to an acquittal, or a more lenient sentence, if convicted.
* Insanity defense
* Procedural defenses
* The fourth and least common of the main types of defenses are procedural defenses. Procedural defenses include things such as entrapment, police fraud, prosecutorial misconduct and denial of a speedy trial. These types of defenses argue that the legal system has failed and the person should therefore be released.
* Collateral estoppel
* Denial of a speedy trial
* Double jeopardy
* Entrapment
* Prosecutorial misconduct
* Selective prosecution
* Innovative defenses
* Innovative defenses are somewhat special types of defenses. They are relatively new and untried, with little or no precedent bearing upon them. Previously tried innovative defenses include "Twinkie defense", "black rage", Asperger's Syndrome and urban survival syndrome. Generally, defendants use these defenses to introduce reasonable doubt into the proceedings. Because of this, precedent could be developed, but probably only when judges refuse to admit evidence of these defenses. At that point, the question becomes one of relevance, and a holding on appeal that such evidence is or is not relevant almost always depends on the facts of the cases. As such, it should not be surprising that the reported cases discuss little of these theories.
# US Criminal Law/Mens rea

* Mens Rea ("guilty mind") is the mental aspect of a crime that describes the criminal defendant's state of mind. The Model Penal Code gives four mens rea categories:
* purposely;
* knowingly;
* recklessly;
* negligently.
* While not used everywhere, those categories are typical. Some crimes (e.g. statutory rape) do not have a mens rea element because they are strict liability crimes.
* Mens Rea (evil intent) is the mental aspect of a crime that describes the criminal defendant's necessary state of mind to constitute a conviction. There are:
* Specific Intent (to commit the crime e.g. assault with intent to commit murder);
* General Intent (most crimes - to do an act that constitutes a crime, a negligent act which leads to the commission of a crime - like speeding which leads to an accident which then results in death or injury to another);
* Violation per se/no intent (such as driving (not recklessly or negligently) above a posted speed limit).
* Transferred Malice
* In both criminal and tort (civil wrong) law, when an intent to cause harm to one person results in harm to another person instead of the intended target, the law transfers the intent to the actual harm.
* So, if Joe meant to kill James, but James ducked and Joe's bullet hits Sue, Joe can be charged with and found guilty beyond a reasonable doubt of the murder of Sue, though he intended to kill James.
# US Criminal Law/Defenses/Consent

Consent involved with entrapment can be defined as law giving an individual and or individuals permission to enter into a situation in which they may or will have to enter some environment participating in unlawful conduct. This permission is allowed to an individual so that evidence and prosecution may be obtained by getting first hand knowledge of a crime without the purpose being known. This consent giving allows immunities to the informant protecting them from prosecution by the law itself. This consent can be considered helpful as well as harmful as the situation the informant is sent to may lead to addiction or later conflicting troubles. This consent can also be used as a legal defense in later circumstances in which the informant cannot be held to full extent of law due to the previous permission giving by the same law. Entrapment is tricky and can be used either way. Depending on the honesty and true intentions set forth to conduct law instructed business.
# US Criminal Law/Defenses/Self defense

Self defense against any entrapping measures can be very tricky. First, are you able too get away or have a definite method too escape what is being forced. Say you have an addiction too a substance and have been clean. You are also having mental and health issues as well as attempting too avoid particular situation. The simple act of saying no 1 time and it being pushed or coerced, shifts entrapment too a form of legal and mental abuse as well as criminal responsibility of another and can be used against the agency operating. If you are forced out of an environment you have too be in by constant tactics too subdue by using unexplainable circumstances, you actually did not intentionally and willingly and maybe also without knowledge break a law. This turns entrapment in a dangerous or unlivable environment and should be took as unconstitutional. Any good agency will get the job done by deesculation and attempting other methods that allowing trusting behavior. Forced bad scenarios make trust issues and legal discrimination
# US Criminal Law

This book is part of a series on US Law:
Civil Procedure Contract Law Copyright Law Corporate Law Criminal Law Federal Rules of Evidence Internet Law Patent Law Tort Law Trademark Law
* This book is about US Criminal Law, its history, development and current state. The book is designed to complement the Wikiversity course of the same name, but can be read on its own. Each chapter begins with an outline of the topic because an understanding of the principles of criminal law is necessary to place the topic in context. Where appropriate each chapter will highlight relevant case law and statutes, which may include links to other resources within and outside Wikimedia wikis.
* The main goals of the book are to enable the reader to:
* understand the aims and functions of the criminal justice system;
* understand the major criminal offences;
* understand the concept of criminal liability;
* critically evaluate the criminal law and reform proposals.
* All crimes have the following four elements in common:
* a voluntary act known as actus reus.
* a culpable state of mind known as mens rea.
* “concurrence” between the mens rea and the actus reus.
* causation of harm (or risk).
Chapters
Mens rea  (2018-01-01)
Actus reus  (2018-01-01)
Summary  (2018-01-01)
Preliminary offenses  (2018-01-01)
Search and seizure  (2018-01-01)
Defenses  (2017-12-31) :
* This book is dual licensed under the GFDL and Creative Commons Attribution-ShareAlike 3.0 Unported License.
# US Criminal Law/Defenses/Denial of a speedy trial

Denial of a speedy trial can occur when the prosecution waits too long to try the defendant. This right is guaranteed by the Sixth Amendment to the United States Constitution and is applied to the states via the Fourteenth Amendment. Klopfer v. North Carolina, 385 U.S. 213 (1967). Barker v. Wingo set out some considerations analyzing speedy trial claims: (1) length of delay, (2) reason for delay, (3) assertion of the right, and (4) prejudice. 407 U.S. 514 (1972).
Factor One: Length of Delay
While there is no hard and fast rule on how long is too long, one rule of thumb is eight months. Courts will generally presume that the delay has been sufficient to satisfy a defendant's prima facie case of the denial of the right to a speedy trial when eight months have passed.
Factor Two: Reason for Delay
Court look to why the trial is delayed: common reasons are laboratory testing delays, overcrowded dockets, and witness unavailability. These will weigh for and against both sides and no hard and fast rule is apparent. The Court will also look at continuances and when and by whom they are requested. Also relevant is whether the continuances were opposed by either party.
Factor Three: Assertion of the Right
A defendant waiting two years to assert his right to a speedy trial will be in a worse position than the defendant who claims it after eight months. Also, a defendant who asks for dismissal instead of a speedily-held trial is not truly asserting his right, but rather is attempting to avoid criminal liability based on delay.
Factor Four: Prejudice
The Court will look to prejudice -- was the defendant harmed by a delay caused by the prosecution. For example, did witnesses die or move away or did their memories fade such that they could no longer be reliable.
Comparison of the Factors:
The Court will weigh the factors for and against a finding that speedy trial rights were violated and will act accordingly. If the Court finds speedy trial rights were violated, it will dismiss the prosecution with prejudice (barring reprosecution). If
# The Computer Revolution/Internet/Digital Certificate

Digital Certificate: Is to authenticate the identity of an individual or organization. They are granted by Certificate Authorities and typically contain the name of the person, organization, or Web site being certified along with a certificate serial number and an expiration date. Digital Certificates also include a public/private key pair. These keys and the digital certificate are used with secure Web pages to guarantee the Web pages are secure and actually belong to the stated organization. This is so users can know for sure who their credit card number or other sensitive data is really being sent to, in order to protect against some online scams.
Security protocols: In order to ensure the security of exchange of certificates between clients and servers, security protocols have been put in place such as SSL and TLS. The role of these protocols is to authenticate clients, authenticate servers, encrypt information being exchanged or ensure the integrity of information is being maintained. Since the encryption of information uses much space and slows the transfers, only the most sensitive transactions such as bank transactions are being encrypted.
# The Computer Revolution/Internet/Communication/What is Webcasting

The word webcast is derived from "web" and "broadcast". Its use has varied over the past decade by different types of organisation and as the nature of the medium came into public use.
The term webcasting was coined when webcast/streaming pioneers Mark Cuban (Audionet), Howard Gordon (Xing Technologies) and Peggy Miles (InterVox Communications) got together with a community of webcasters to pick a term to describe the technology of sending audio and video on the Net...that might make sense to people. The term netcasting was a consideration, but one of the early webcast community members owned a company called NetCast, so that term was not used, seeking a name that would not be branded to one company. Discussions were also conducted about the term with the National Association of Broadcasters for their books - Internet Age Broadcaster I and II, written by Peggy Miles and Dean Sakai.
The generally accepted use of the term webcast is the "transmission of linear audio or video content over the Internet".
A webcast uses streaming media technology to take a single content source and distribute it to many simultaneous listeners/viewers.
The largest "webcasters" include existing radio and TV stations who "simulcast" their output, as well as a multitude of Internet only "stations". The term webcasting is usually reserved for referring to non-interactive linear streams or live events.
Rights and licensing bodies offer specific "Webcasting licenses" to those wishing to carry out Internet broadcasting using copyright material.
Webcasting is also used extensively in the commercial sector for investor relations presentations (such as Annual General Meetings), in E-learning (to transmit seminars), and for related communications activities. However, webcasting does not bear much, if any, relationship to the idea of Web conferencing which is designed for many-to-many interaction.
The ability to webcast using cheap/accessible technology has allowed independent media to flourish. There are many notable independent shows that broadcast regularly online. Often produced by average citizens in their homes they cover many interests and topics; from the mundane to the bizarre. Webcasts relating to computers, technology, and news are particularly popular and many new shows are added regularly.
# The Computer Revolution/Intellectual Properties

Intellectual Property Rights exist to make sure people do not unfairly mistreat, misrepresent, misuse or claim ownership of other people's work. Intellectual property rights include copyrights, trademarks, and the patenting of inventions, products, processes, and procedures.
DRM (Digital Rights Management) and proprietary formats can restricts the ability to study, duplicate, transform and use things such as software, music, photography, or movies. This type of practices also can increase the cost of production and therefore the final product and will endanger historic records and future access to the works as they become public domain. They transform ownership into licensing.
Digital watermarks can be placed on top of digital work to display copyright or ownership while still showcasing the work. Note that recent changes in international copyright law makes it unnecessary to specifically state ownership. Watermarking became useful especially in images with the rise of the Internet.
A trademark or service mark is a word, symbol, phrase, or design (or combination of them) that is specifically assign to a particular product or service, which distinguishes it from other goods or services; also referred to as a brand name. There are several different symbols that can be used with trademarks (marks on the top, at the end of a logo or a phrase):
TM-for trademarks that are claimed but not registered with U.S. Patent and Trademark Office;
SM-for nonregistered service marks;
R (with a circle around it)-for registered trademarks and service marks.
Trademarks last 10 years, but they can be renewed as many times as anticipated, as long as they are being used in commerce. Although federal registration of a mark is not mandatory, it has several advantages, including notice to the public of the registrant's claim of ownership of the mark, in addition trademark law protects domain names associated with business’s trademark, like Amazon.com for instance.
Source: “Understanding Computers-Today and Tomorrow”-D. Morley, C. Parker (Chapter 16, pg. 635).

## Printing Labs Scared of Copyright Infringement

Printing Labs worried about copyright infringement are refusing to print digital photos if they look too “professional.” Stores around the country including Wal-Mart and Walgreens are choosing to err on the side of caution. If a photo looks too high quality (and keep in mind this is a very subject decision) then the lab will refuse to print it. This poses a problem when most cameras are now equipped (sometimes even cell phones) to capture extraordinarily high quality photos. It has become harder to distinguish between professional art and a photo that someone took of a flower in their backyard. The current law dates back to the 1970s and is not applicable in today’s society. Many customers will continue to face an uphill battle trying to get their photos printed until something is done to further clarify the law.
Retrieved from http://www.usatoday.com/tech/news/2005-06-16-digital-picture-problems_x.htm on April 25, 2012.