started work on introduction and background

main.bib

@@ -1305,3 +1305,40 @@ For additional {GBD} results and resources, visit the {GBD} 2019 Data Resources
 	date = {1992-05},
 	langid = {english},
 }
+
+@online{pedroso_menstrual_2022,
+	title = {The Menstrual Cycle},
+	url = {https://kindbody.com/the-menstrual-cycle/},
+	abstract = {Fertility, gynecology, and wellness services in modern, tech-enabled clinics. Best-in-class care, accessible pricing, and a seamless patient experience.},
+	titleaddon = {Kindbody},
+	author = {Pedroso, Dr Jasmine},
+	urldate = {2025-03-10},
+	date = {2022-06-03},
+	file = {Snapshot:/home/alex/Zotero/storage/738JEKW7/the-menstrual-cycle.html:text/html},
+}
+
+@article{silberstein_physiology_2000,
+	title = {Physiology of the Menstrual Cycle},
+	volume = {20},
+	rights = {https://journals.sagepub.com/page/policies/text-and-data-mining-license},
+	issn = {0333-1024, 1468-2982},
+	url = {https://journals.sagepub.com/doi/10.1046/j.1468-2982.2000.00034.x},
+	doi = {10.1046/j.1468-2982.2000.00034.x},
+	abstract = {The normal female life cycle is associated with a number of hormonal milestones: menarche, pregnancy, contraceptive use, menopause, and the use of replacement sex hormones. All these events and interventions alter the levels and cycling of sex hormones and may cause a change in the prevalence or intensity of headache. The menstrual cycle is the result of a carefully orchestrated sequence of interactions among the hypothalamus, pituitary, ovary, and endometrium, with the sex hormones acting as modulators and effectors at each level. Oestrogen and progestins have potent effects on central serotonergic and opioid neurons, modulating both neuronal activity and receptor density. The primary trigger of menstrual migraine appears to be the withdrawal of oestrogen rather than the maintenance of sustained high or low oestrogen levels. However, changes in the sustained oestrogen levels with pregnancy (increased) and menopause (decreased) appear to affect headaches. Headaches that occur with premenstrual syndrome appear to be centrally generated, involving the inherent rhythm of {CNS} neurons, including perhaps the serotonergic pain-modulating systems.},
+	pages = {148--154},
+	number = {3},
+	journaltitle = {Cephalalgia},
+	author = {Silberstein, S D and Merriam, G R},
+	urldate = {2025-03-10},
+	date = {2000-04},
+	langid = {english},
+	file = {Full Text:/home/alex/Zotero/storage/EL585H2P/Silberstein and Merriam - 2000 - Physiology of the Menstrual Cycle.pdf:application/pdf},
+}
+
+@artwork{wikimedia_commons_basic_2019,
+	title = {Basic Female Reproductive System},
+	url = {https://en.wikipedia.org/wiki/File:Basic_Female_Reproductive_System_(English).svg},
+	author = {Wikimedia Commons},
+	date = {2019},
+	file = {background_female_reproductive_organs:/home/alex/Zotero/storage/5MAJ4CG5/background_female_reproductive_organs.png:image/png},
+}

notebooks/requirements.txt

@@ -0,0 +1,5 @@
+pandas
+numpy
+matplotlib
+jupyter
+notebook

thesis/main.tex

@@ -6,7 +6,10 @@
 
 % Packages
 \usepackage{amsmath}
-% biber bibliography
+
+\usepackage{graphicx}
+\graphicspath{{resources/figures/}}
+
 \usepackage[style=ieee, backend=biber]{biblatex}
 \addbibresource{../main.bib}
 
@@ -18,19 +21,19 @@
     % university and faculty
     \maketitle
 
-    \include{sections/introduction/introduction}
+    \include{sections/introduction}
 
-    \include{sections/background/background}
+    \include{sections/background}
 
-    \include{sections/related_work/related_work}
+    \include{sections/related_work}
 
-    \include{sections/methodology/methodology}
+    \include{sections/methodology}
 
-    \include{sections/results/results}
+    \include{sections/results}
 
-    \include{sections/discussion/discussion}
+    \include{sections/discussion}
 
-    \include{sections/conclusion/conclusion}
+    \include{sections/conclusion}
 
     \printbibliography
 

thesis/sections/background.tex

@@ -0,0 +1,87 @@
+%! Author = alex
+%! Date = 3/7/25
+
+
+\section{Background}\label{sec:background}
+
+\subsection{Physiological Background}\label{subsec:physiological_background}
+\subsubsection{Menstrual Cycle}\label{subsec:menstrual_cycle}
+The menstrual cycle describes the physiological changes in the female body that prepare it for pregnancy.
+It is divided into two phases: the \textbf{follicular phase} and the \textbf{luteal phase}.
+\\
+During the follicular phase, the ovarian follicles mature, and the endometrium (the inner lining of the uterus) thickens
+in preparation for a potential implantation of a fertilized egg.
+Around day 14 of a typical cycle, ovulation occurs, marking the transition to the luteal phase.
+Ovulation refers to the rupture of the mature ovarian follicle and the release of an egg cell into the fallopian tube.
+Figure\ref{fig:background_basic_female_reproductive_system} illustrates the female reproductive system,
+including the ovaries and the fallopian tubes.
+\\
+\begin{figure}
+    \centering
+    \includegraphics[width=0.4\textwidth]{background_female_reproductive_organs}
+    \caption{The basic female reproductive system\cite{wikimedia_commons_basic_2019}.}
+    \label{fig:background_basic_female_reproductive_system}
+\end{figure}
+Ovulation is triggered by a surge in \textbf{luteinizing hormone (LH)}
+and \textbf{follicle-stimulating hormone (FSH)}, following a peak in estradiol levels.
+As ovulation occurs, estradiol levels drop, progesterone levels begin to rise and a slight increase in body temperature
+(typically around 0.5°C) can be observed.
+This marks the beginning of the luteal phase.
+\\
+During the luteal phase, the endometrium thickens further, creating an optimal environment for embryo implantation.
+LH and FSH levels decrease, while progesterone remains elevated to support endometrial maintenance.
+If fertilization does not occur, progesterone levels drop, leading to the shedding of the endometrial lining along
+with the unfertilized egg.
+This process, known as menstruation, marks the beginning of a new cycle.
+\\
+The menstrual cycle typically lasts around 28 days, with ovulation occurring near the midpoint.
+However, variations, particularly in the follicular phase length, are common and can be influenced by factors such as stress, diet, exercise and age\cite{silberstein_physiology_2000}.
+Figure~\ref{fig:background_menstrual_cycle_physiology} provides a detailed overview of the hormonal and physiological changes
+throughout the menstrual cycle.
+
+\begin{figure}
+    \centering
+    \includegraphics[width=0.7\textwidth]{background_menstrual_cycle_physiology}
+    \caption{Physiological changes during the menstrual cycle\cite{pedroso_menstrual_2022}.}
+    \label{fig:background_menstrual_cycle_physiology}
+\end{figure}
+
+\subsubsection{Fertility Prediction}\label{subsec:fertility_prediction}
+Throughout the menstrual cycle, the chance of fertilization varies significantly.
+An egg cell released from the ovary during ovulation, can be fertilized for up to 24 hours.
+However, since male sperm cells can survive up to 6 days inside the female reproductive tract,
+the fertile window is typically defined as the five days before ovulation until one day after ovulation\cite{dunson_day-specific_1999}.
+Research by \citeauthor{dunson_day-specific_1999} has shown that the highest chance of fertilization is around one day before ovulation,
+as illustrated in Figure~\ref{fig:background_pregnancy_chance}.
+
+\begin{figure}
+    \centering
+    \includegraphics[width=0.8\textwidth]{background_pregnancy_chance_over_time}
+    \caption{Chance of fertilization depending on the day of the menstrual cycle.
+    The highest chance is around one day before ovulation\cite{dunson_day-specific_1999}.}
+    \label{fig:background_pregnancy_chance}
+\end{figure}
+
+It is important to note that fertility prediction is inherently dependent on ovulation prediction.
+Since the probability of conception is tightly linked to ovulation timing, the accuracy of fertility prediction methods
+is constrained by the precision of ovulation detection.
+This relationship underscores the necessity of developing reliable ovulation prediction models,
+as even small inaccuracies can significantly impact fertility assessments.
+
+\subsubsection{Physiological Signs of Ovulation}\label{subsec:physiological_signs}
+Several physiological signs correlate with ovulation and can be used for prediction.
+As shown in Figure~\ref{fig:background_menstrual_cycle_physiology}, these include hormonal fluctuations (LH and FSH surges) and
+changes in body temperature.
+Additionally, variations in cervical mucus consistency, salivary ferning patterns,
+and electrical resistance of the skin and vaginal mucosa have been observed\cite{silberstein_physiology_2000}.
+
+Among these, ultrasonography provides the most accurate confirmation of ovulation by detecting follicular changes,
+but it is costly and requires specialized equipment.
+Hormone measurements in urine and blood are widely used and available in at-home test kits,
+but they require frequent testing.
+Temperature-based methods, particularly body temperature tracking, offer a non-invasive alternative by
+detecting the slight temperature rise that follows ovulation.
+Advances in wearable technology have further enabled continuous and automated temperature monitoring,
+improving accessibility and usability\cite{alexander_fertilitatsmonitoring_2014, luo_detection_2020, yu_tracking_2022}.
+
+\subsection{Technical Background}\label{subsec:technological_background}

thesis/sections/background/background.tex

@@ -1,14 +0,0 @@
-%! Author = alex
-%! Date = 3/7/25
-
-\section{Background}\label{sec:background}
-
-
-\subsection{Menstrual Cycle}\label{subsec:menstrual_cycle}
-The ovulation is defined as the rupture of the ovarian follicle and the release of an egg cell into the fallopian tube.
-There, the egg cell can be fertilized by sperm cells and develop into an embryo\cite{holesh_physiology_2025}.
-This is accompanied by changes in the fluxing gonadotropin-releasing hormone (GnRH), luteinizing hormone (LH),
-and follicle-stimulating hormone (FSH) levels in the blood.
-Additionally, the basal body temperature (BBT) rises by about 0.5 degrees Celsius after ovulation.
-
-% explain different physiological signs usable for prediction, advantages and disadvantages

thesis/sections/methodology.tex

@@ -0,0 +1,8 @@
+%! Author = alex
+%! Date = 3/6/25
+
+\section{Methodology}\label{sec:methodology}
+
+% why did I select tft over other methods -> include examples of time series and why I belief a complex model could help
+% you did I apply it
+% implementation details

thesis/sections/methodology/methodology.tex

@@ -1,4 +0,0 @@
-%! Author = alex
-%! Date = 3/6/25
-
-\section{Methodology}\label{sec:methodology}

thesis/sections/related_work.tex

@@ -0,0 +1,7 @@
+%! Author = alex
+%! Date = 3/6/25
+
+\section{Related Work}\label{sec:related_work}
+
+
+%parts: traditional methods, ml approaches, tft in medical time series or other time series

thesis/sections/related_work/related_work.tex

@@ -1,4 +0,0 @@
-%! Author = alex
-%! Date = 3/6/25
-
-\section{Related Work}\label{sec:related_work}