ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications.

BACKGROUND: Processing raw genomic data for downstream applications such as imputation, association studies, and modeling requires numerous third-party bioinformatics software tools. It is highly time-consuming and resource-intensive with computational demands and storage limitations that pose significant challenges that increase cost. The use of software tools independent of one another, in a disjointed stepwise fashion, increases the difficulty and sets forth higher error rates because of fragmented job executions in alignment, variant calling, and/or build conversion complications. As sequencing data availability grows, the ability for biologists to process it using stable, automated, and reproducible workflows is paramount as it significantly reduces the time to generate clean and reliable data. RESULTS: The Iliad suite of genomic data workflows was developed to provide users with seamless file transitions from raw genomic data to a quality-controlled variant call format (VCF) file for downstream applications. Iliad benefits from the efficiency of the Snakemake best practices framework coupled with Singularity and Docker containers for repeatability, portability, and ease of installation. This feat is accomplished from the onset with download acquisitions of any raw data type (FASTQ, CRAM, IDAT) straight through to the generation of a clean merged data file that can combine any user-preferred datasets using robust programs such as BWA, Samtools, and BCFtools. Users can customize and direct their workflow with one straightforward configuration file. Iliad is compatible with Linux, MacOS, and Windows platforms and scalable from a local machine to a high-performance computing cluster. CONCLUSION: Iliad offers automated workflows with optimized time and resource management that are comparable to other workflows available but generates analysis-ready VCF files from the most common datatypes using a single command. The storage footprint challenge of genomic data is overcome by utilizing temporary intermediate files before the final VCF is generated. This file is ready for use in imputation, genome-wide association study (GWAS) pipelines, high-throughput population genetics studies, select gene candidate studies, and more. Iliad was developed to be portable, compatible, scalable, robust, and repeatable with a simplistic setup, so biologists that are less familiar with programming can manage their own big data with this open-source suite of workflows.

The kinesthetic diagnosis in a homeric item of pathological heartbeat: An overview in the history of ancient greek medicine.

The Iliad, by the Greek poet Homer, is a precious mine of examples of war traumatology. In the specific case of spear wounds in the chest, the death of the Trojan warrior Alcathous is particularly interesting from the point of view of the history of medicine and the evolution of cardiology and knowledge of the heart at the time of ancient Greece. In particular this paper aims to evidence and reconstruct the main anatomical and physiological knowledge of the heart at that time. Indeed, a historical-linguistic analysis of the Greek text prompts some reflections and thoughts on the heartbeat in pathological conditions and on the function of the heart as a hematopoietic organ. Furthermore, Homer's account is a critical text that highlights the relevance of the use of the senses in the ancient description of nosological pictures and it allows us an interesting and suggestive approach to reconstruction from the historical and historiographical point of view.

War trauma in Homer's Iliad: a trauma registry perspective.

PURPOSE: Homer's Iliad reports detailed descriptions of war traumas, with precise anatomical references, so that the Iliad can be considered the first trauma registry. We aimed to analyse the Iliad from the perspective of a modern trauma registry: that is, to find historical and local prognostic factors through the epidemiological study of the reported traumas. METHODS: Two different editions of Homer's Iliad-one in English and one in Italian-were thoroughly studied and epidemiological data were statistically analysed. RESULTS: 148 reports of human traumas were analysed. The majority of traumas (73.6%) involved Trojan warriors, with spears being the most frequent wounding agent (71%). Overall mortality was 84.5% and was higher in the Trojan field (90.8% vs 61.5%). Despite the high mortality, median New Injury Severity Score (NISS) was low, probably due to high prevalence of penetrating mono-systemic trauma. Median NISS was higher in the Trojan group. Compared to the Achaeans, the Trojans had more torso injuries, whereas Achaeans had more injuries to limbs and superficial tissues. However, in both fields, head and neck were more frequently injured. CONCLUSIONS: Homer's Iliad gives us an interesting insight into war traumas during the siege of Troy. The reported higher mortality within the Trojan army can be explained not only by poetic reasons but also by different military skills.

Head Injuries in Homer's Iliad.

The Iliad is an epic poem chronicling the journey of Achilles in the Trojan War. The poem is one of the earliest sources of written literature in the Western canon. It is not a medical text, but the many and varied descriptions of injuries and their consequences mean that it is an important source for examining the earliest notions of anatomy and knowledge of the pathologies that result from trauma. Head injuries feature prominently in the text and represent written accounts of neurotrauma from nearly 3000 years ago. Previous work on the poem has suggested an awareness of neurological concepts such as nystagmus, syncope, and pupillary dilatation after trauma. In this paper, we identify and categorize all of the head injuries detailed in the text and examine these to identify concepts of functional neuroanatomy that are revealed by the descriptions. We identify and discuss 2 detailed descriptions of head injury, suggesting an awareness of decerebrate posturing after brainstem injury and cerebrospinal fluid leakage following a basal skull fracture.

Machaon, Son of Asclepius, the Father of Surgery.

The first description of organized surgical care is given in Homer's epic poem "Iliad'', even though evidence of performing surgical operations can be traced back to the history of ancient civilizations. Machaon (ca. 1300 BC), the son of Asclepius, was described as a skillful and confident therapist, whose lineage ensured a unique training. He lived in an era when the reality was shaped by myths, and natural phenomena were ruled by the will of the Olympian gods. It was at that time when philosophers and scientists rediscovered the world that surgery was born. We review and present Machaon's story, as he is not only the first documented surgeon ever mentioned in written records in Greek history, but he also proved himself to be a valiant soldier at the battlefield, during the Trojan War. It is no wonder that the life of such a charismatic man, living in a place and time of prosperity and steady evolution of both the scientific and the spiritual world, became a demigod patron of surgical treatment and a landmark in the history of medicine.

Achilles: A Homeric hero enamoured with the absolute.

This article explores through a psychoanalytical lens the character of Achilles in Homer's Iliad, the matrix behind the Western conception of heroism. The contribution reveals the psychological link binding the words and acts of the most valiant of warriors in Antiquity, which is situated in myth and termed "the Eros of the absolute." The paroxystic ideality underlying the aforementioned myth, which is rooted in the anthropological need to believe, is at the origin of Achilles' legendary µá¿†νις, that is, the flood of rage triggered by contests for supremacy, aggravated by the loss of his war comrade, aroused by the drama of aging and death, and then transfigured through song and memory. The main claim of the author is that Iliad, despite its seeming lack of attention to interiority, is launched by the archetypal emotion of wrath and owes its appeal to its hero's embrace of heroic idealism in an excessive, radical and absolute way that results in a captivating narcissism and sadomasochistic antithesis of ideality. This argument leads to the conclusion that Homer is the Father of the "primitive horde" of affects.

Achilles: A Homeric hero enamoured with the absolute.

This article explores through a psychoanalytical lens the character of Achilles in Homer's Iliad, the matrix behind the Western conception of heroism. The contribution reveals the psychological link binding the words and acts of the most valiant of warriors in Antiquity, which is situated in myth and termed "the Eros of the absolute." The paroxystic ideality underlying the aforementioned myth, which is rooted in the anthropological need to believe, is at the origin of Achilles' legendary µá¿†νις, that is, the flood of rage triggered by contests for supremacy, aggravated by the loss of his war comrade, aroused by the drama of aging and death, and then transfigured through song and memory. The main claim of the author is that Iliad, despite its seeming lack of attention to interiority, is launched by the archetypal emotion of wrath and owes its appeal to its hero's embrace of heroic idealism in an excessive, radical and absolute way that results in a captivating narcissism and sadomasochistic antithesis of ideality. This argument leads to the conclusion that Homer is the Father of the "primitive horde" of affects.

Trauma management in Homer's Iliad.

Homer's Iliad is one of the highest intellectual products of the early ancient Greek civilisation. A plethora of medical information lies within Iliad's 24 rhapsodies, and a total of 147 injuries are described. The present study records and evaluates all cases of trauma management included in this epic poem. Not only Iliad's original text but also all myths related to Iliad from the five-volume Greek Mythology by Ioannis Kakridis were meticulously studied to locate the injured person, the type of trauma, the care provider and the type of given care as well as the outcome of each case. A total of 21 cases were found and evaluated with a 5% mortality rate. The majority of these injuries were caused by an arrow (43%) and were located to the upper extremity (43%). Injuries of the head, neck and trunk were not treated as all of them were lethal. Many of the recorded trauma management techniques can be correlated to modern medicine. Furthermore, the role and skills of military doctors and paramedics, mentioned by Homer, is discussed.

Helmet Use and Head Injury in Homer's Iliad.

BACKGROUND: Homer's detailed descriptions of head injuries inflicted during the Trojan War are of particular interest to individuals in the medical community. Although studies have examined the prevalence of such injuries, none have examined the preventive measures taken to avoid them. An in-depth review of helmet use in Homer's Iliad was conducted to address this previously unexplored facet of the epic. METHODS: An English translation of Homer's text was reviewed for all references to helmet use. The number of helmet references in each book was recorded, along with other pertinent details for each reference. RESULTS: There were 87 references to helmets (40 combat, 47 noncombat). The helmet belonged to a Greek warrior in 41 cases (47.1%), a Trojan warrior in 38 cases (43.6%), a divinity in 5 cases (5.7%), and a general group of warriors in 3 cases (3.4%). Helmet use provided protective benefit to Greek warriors at a rate of 30.0% (3 of 10) and Trojan warriors at a rate of 11.1% (2 of 18). This difference was not statistically significant (P = 0.23). The overall combined protective benefit of helmet use in the text was 17.9% (5 of 28). Helmets belonging to 15 specific Greek warriors and 18 specific Trojan warriors were referenced in the text. Helmets belonging to Hector (n = 12) and Achilles (n = 8) were most frequently mentioned. CONCLUSIONS: Helmet use and head injury both play a prominent role in Homer's Iliad. Helmets are frequently used in combat settings but with relatively little success. Helmets are also used in various noncombat settings.

Desaparecidos: uma história de dor / The missing ones: a history of pain / Desaparecidos: una historia de dolor / Disparus: une histoire de douleur

Assombrado pela extensa lista de desaparecidos que as ditaduras latino-americanas impingiram a pais, mães e companheiros, o autor relê uma das obras fundadoras da civilização ocidental - a Ilíada - e tenta compreender por que os gregos e os troianos lutam furiosamente para reaver o corpo de seus mortos. Desrespeitar um cadáver indigna os próprios deuses. Não poder lhe render as homenagens fúnebres é uma hipótese nem sequer cogitada. O quase impossível trabalho do luto requer o corpo, afirma o autor. Sem ele, não se criam os sonhos nem as narrativas. Nem a melancolia pode se instalar. Cria-se no espírito um buraco negro que, como um parasita, atrai para si o pensamento e os afetos e impede a vida de prosseguir. No plano da cultura e da história ocorrerá a mesma deformação que se abate sobre os destinos individuais.

Horrified by the extensive list of missing people that the Latin American dictatorships imposed to parents, spouses and domestic partners, the author rereads one of the founding works of Western civilization - The Iliad - and tries to understand why the Greeks and the Trojans fight furiously in order to get back the bodies of their dead ones. Disrespecting a corpse outrages the Gods themselves. Not being able to deliver a proper eulogy and funeral is not even a ventured hypothesis. The almost impossible grief work requires the body, the author writes. Without it, dreams and narratives are not created. Neither melancholy can take place. A black whole is created in the spirit; as a parasite, this black whole attracts thought and affections to itself, and it does not let life go on. In the cultural and historical fields, there will be the same deformation that impacts their individual destinies.

Asombrado por la extensa lista de desaparecidos que las dictaduras latinoamericanas endosaron a padres, madres y compañeros, el autor relee una de las obras fundadoras de la civilización occidental - la Ilíada - e intenta comprender por qué griegos y troyanos luchan furiosamente para recuperar el cuerpo de sus muertos. La falta de respeto hacia el cadáver causa indignación a los propios dioses. No rendirle los homenajes fúnebres es una hipótesis fuera de cogitación. El casi imposible trabajo de luto requiere el cuerpo, afirma el autor. Sin él, no se crean sueños ni narrativas. Ni siquiera se puede instalar la melancolía. Se crea un agujero negro en el espíritu que -como un parásito- atrae hacia sí el pensamiento y los afectos impidiendo que la vida prosiga. En los planos de la cultura y de la historia sucederán las mismas deformaciones que se abaten sobre los destinos individuales.

Étonné par la longue liste de disparus que les dictatures latino-américaines ont imposé aux pères, mères et compagnons, l'auteur relit une des œuvres fondatrices de la civilisation occidentale - l'Iliade - et essaye de comprendre pourquoi les grecs et les troyens se battent furieusement pour reprendre le corps de leurs morts. Violer un cadavre dégoûte les propres dieux. Ne pas pouvoir lui rendre les hommages funèbres est une hypothèse pas même pensée. Le presque impossible travail du deuil requiert le corps, déclare l'auteur. Sans lui, on ne crée pas les rêves ni les récits. Ni même la mélancolie ne peut s'installer. On crée dans l'esprit un trou noir qui, comme un parasite, lui attire la pensée et les affects et qui empêche la vie de poursuivre. Sur le plan de la culture et de l'histoire aura lieu la même déformation qui s'abat sur les destins individuels.

Hecamede: Homeric nurse of the battle-wounded in the Trojan War.

The Homeric epics present the 10-year lasting Trojan War, offering the description of battle wounds and medical care of injuries. Hecamede is referred by the Homer as a battlefield nurse who had knowledge of the treatment of bleeding battle wounds.

Upper extremity injuries in Homer's Iliad.

Homer's Iliad remains a fascinating source of medical history. This epic poem, compiled around 800 BCE, describes several weeks of the last year of the 10-year siege of Troy (Ilion) by the Achaeans. Homer composed the epic by combining and formalizing oral poems, legends, customs, and experiences that originated in the later Mycenaean age (1600-1100 bce). The story centers on the rage of the great warrior Achilles. The Iliad remains the oldest record of Greek medicine and a unique source of surgical history. This study examines the upper extremity injuries described in the Iliad and compares them to those other sites of injury.

Anxiety disorders in ancient Indian literature.

In western literature, the oldest description of symptoms of PTSD, an anxiety group of disorder, is seen in Homer's Iliad written around 720 BC. According to Shay, Achilles was suffering from symptoms of PTSD. However, in the Indian literature it was mentioned around 5000 BC. The description of a PTSD-like syndrome is seen in the Ramayana, although it was not described as PTSD or by any other similar name. Ravana's brother Marrich was having symptoms of PTSD after he was grievously hurt by Lord Rama's arrow and was almost dead. This traumatic event threatened his physical integrity. He developed all the symptoms of PTSD, like hyper-arousal, re-experiencing the events and avoidance. He also gave up his natural work of harassing the monk and got engaged in meditation and austerities. His symptoms lasted for many years till Lord Rama killed him, while he was masquerading as a golden deer to deceive Sita. In another ancient epic Shrimad Bhagavatam, Maharshi Ved Vyasa described the symptoms of Generalized Anxiety Disorder (GAD). The demon King Kansha developed GAD-like symptoms, when Lord Krishna killed all his demons and threatened to kill him. He developed symptoms of GAD, like excessive worry about the attack from his arch foe Krishna, difficulty in concentration and difficulty in falling asleep. Like Marrich, the symptoms of Kansha also lasted until Lord Krishna killed him.

The death of Hector: pity in Homer, empathy in medical education.

Empathy is thought a desirable quality in doctors as a key component of communication skills and professionalism. It is therefore thought desirable to teach it to medical students. Yet empathy is a quality whose essence is difficult to capture but easy to enact. We problematise empathy in an era where empathy has been literalised and instrumentalised, including its measurement. Even if we could agree a universally acceptable definition of empathy, engendering it in the student requires a more subtle approach than seems the case currently. We therefore examine this modern concept and compare it with others such as pity and compassion, using the medium of Homer's Iliad. Two famous scenes from the Iliad elicit pity in the characters and the audience. Pity and compassion are, however, given a complexity within the narrative that often seems lacking in modern ways of conceptualising and teaching empathy.

Putting it bluntly: communication skills in the Iliad.

In current undergraduate medical curricula, much emphasis is placed on learning the skills of communication. This paper looks at Homer's Iliad and argues that from it we may learn that our skills can be mechanistic, shallow and simplistic. Homer was regarded in the Greek and Roman world as the father of rhetoric. This reputation rested greatly on book 9 of the Iliad, the embassy from the Greek leaders to the bitter, wrathful Achilles. The mission of the three emissaries is to persuade him to return to the ranks of the Greeks, who are being routed since his refusal to fight. We learn how the outcome of a conversation may be predetermined by the previous relationship of the speakers, and how a man beyond reason responds to reason; we should reflect that Homer's audience heard the piece knowing the outcome, giving it a tragic inevitability. We, the audience, cannot analyse the discourse rationally, because in this, as in all communication, reason is disturbed by emotion.