Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data.

We investigate alternative strategies against reference bias and postmortem damage in low coverage paleogenomes. Compared to alignment to the linear reference genome, we show that masking known polymorphic sites and graph alignment effectively remove reference bias, but only starting from raw read files. We next study approaches to overcome postmortem damage: trimming, rescaling, and our newly developed algorithm, bamRefine (github.

The Population History of Domestic Sheep Revealed by Paleogenomes.

Sheep was one of the first domesticated animals in Neolithic West Eurasia. The zooarchaeological record suggests that domestication first took place in Southwest Asia, although much remains unresolved about the precise location(s) and timing(s) of earliest domestication, or the post-domestication history of sheep. Here, we present 24 new partial sheep paleogenomes, including a 13,000-year-old Epipaleolithic Central Anatolian wild sheep, as well as 14 domestic sheep from Neolithic Anatolia, two from Neolithic Iran, two from Neolithic Iberia, three from Neolithic France, and one each from Late Neolithic/Bronze Age Baltic and South Russia, in addition to five present-day Central Anatolian Mouflons and two present-day Cyprian Mouflons.

READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics.

The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy.

The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus).

We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced to a coverage of 0.6-6.4×.

Benchmarking kinship estimation tools for ancient genomes using pedigree simulations.

There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.

Eltrombopag treatment in thrombocytopenia following hematopoietic stem cell transplantation: A multicenter real-world experience.

Introduction: Thrombocytopenia is among the most common complications following hematopoietic stem cell transplantation and is associated with increased mortality and morbidity with no standard treatment yet. In this multicenter and retrospective study, we aim to present our multi-center experience of Eltrombopag treatment in patients with isolated thrombocytopenia following HSCT.

Material-method: A total of 73 patients from 5 centers who underwent autologous or allogeneic stem cell transplantation, had no primary disease relapse, all of whom had neutrophil engraftment, complete chimerism, and who were diagnosed with Prolonged Isolated Thrombocytopenia (PIT) or Secondary Failure Of Platelet Recovery (SFPR) were included in the study.

Effects of Oxytocin on Glutamate Mediated Neurotoxicity in Neuroblastoma Cell Culture.

Introduction: We aimed to investigate the effects of oxytocin on neurite growth, cell viability, cell proliferation and apoptosis to demonstrate its neuroprotective effect on glutamate induced neurotoxicity in human neuroblastoma SH-SY5Y cell culture.

Method: The effect of oxytocin on the toxic effects of glutamate in human neuroblastoma SH-SY5Y cell line with the Neurotoxicity Screening Test (NTT), apoptotic effects by Terminal Transferase dUTP Nick End Labeling (TUNEL) method and cell viability test by 3-(4.5-dimethylthiazol-2-yl)-2.

Voltammetric determination of Molnupiravir used in treatment of the COVID-19 at magnetite nanoparticle modified carbon paste electrode.

To reduce the progression of the viral process in patients infected with COVID-19, new treatments and drug active substances are needed. One of these drugs is Molnupiravir (MNP) which has a direct antiviral effect and has also proven to be highly effective in reducing the azopharyngeal SARS-CoV-2 infectious virus and viral RNA. Due to the importance and frequent use of this drug in the treatment of COVID-19, its accurate, quick, and cheap detection in pharmaceutical or biological samples is crucial.

A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition.

Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal BCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data.

Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication.

Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies.

Technique for Adaptation of Konno Aortoventriculoplasty in Patient-Prosthesis Mismatch.

The patient-prosthesis mismatch has been reported as an important cause of adverse outcome following aortic valve replacement. The relief of patient-prosthesis mismatch generally requires a reoperation of comprehensive nature, which necessitates an extensive aortic root enlargement. The Konno aortoventriculoplasty represents an efficient treatment option, as this technique provides both extreme root enlargement and relief of the frequently associated subvalvular obstruction.

Human inbreeding has decreased in time through the Holocene.

The history of human inbreeding is controversial. In particular, how the development of sedentary and/or agricultural societies may have influenced overall inbreeding levels, relative to those of hunter-gatherer communities, is unclear. Here, we present an approach for reliable estimation of runs of homozygosity (ROHs) in genomes with ≥3× mean sequence coverage across >1 million SNPs and apply this to 411 ancient Eurasian genomes from the last 15,000 years.

Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.

The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic, mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings, household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Aşıklı Höyük and Çatalhöyük.

Rerouting anomalous coronary artery origin in aortopulmonary window in newborn.

Coronary artery anomalies may accompany the aortopulmonary window and, if not noticed, may cause catastrophic consequences. The repair of the aortopulmonary window is quite straightforward; however, establishing a normal coronary pattern may challenge the repair. When the anomalous origin of the coronary artery is on the defect rim, right at the location where sutures are to be placed, it may interfere with proper suture placement.

Birth outcomes after inadvertent use of category X drugs contraindicated in pregnancy: Where is the real risk?

Öztürk Z, Ölmez E, Gürpınar T, Vural K. Birth outcomes after inadvertent use of category X drugs contraindicated in pregnancy: Where is the real risk? Turk J Pediatr 2018; 60: 298-305. Drugs contraindicated in pregnancy are medicines that should be avoided by pregnant women, since they carry a concern for teratogenicity or there is no indication for their use during pregnancy.

Association of preoperative plasma fibrinogen level with postoperative bleeding after on-pump coronary bypass surgery: does plasma fibrinogen level affect the amount of postoperative bleeding?

Objectives: Our primary aim was to investigate the association between the preoperative concentration of plasma fibrinogen and the volume of postoperative bleeding. Our secondary aim was to identify whether there is a possible correlation between the patients' different characteristics and haemostatic laboratory variables and the postoperative amount of bleeding after on-pump coronary artery bypass grafting procedures.

Methods: A total of 550 adult patients undergoing isolated coronary artery bypass grafting on cardiopulmonary bypass in our hospital were enrolled and investigated retrospectively.

In vitro investigation of the effect of matrix molecules on the behavior of colon cancer cells under the effect of geldanamycin derivative.

The chaperone-binding drug, 17-allylamino-17-demethoxygeldanamycin, has recently come into clinical use. It is a derivative of geldanamycin, an ansamycin benzoquinone antibiotic with anti-carcinogenic effect. Understanding the effect of this drug on the cancer cells and their niche is important for treatment.